scHOT analysis of Mouse Olfactory Bulb data
Shila Ghazanfar
26/10/2019
Set up
source("../functions.R")
tol12qualitative=c("#332288", "#6699CC", "#88CCEE", "#44AA99", "#117733", "#999933", "#DDCC77", "#661100", "#CC6677", "#AA4466", "#882255", "#AA4499")
if (!file.exists("output")) {
system("mkdir output")
}
parallel = TRUE
ncores = 10Load packages
if (!require(DCARS)) {
library(devtools)
devtools::install_github("shazanfar/DCARS")
}
library(DCARS)
library(ggplot2)
library(gplots)
library(SingleCellExperiment)
library(scater)
library(scran)
library(reshape)
library(scattermore)
library(dynamicTreeCut)
library(ComplexHeatmap)
library(GO.db)
library(org.Mm.eg.db)
library(stringr)
library(matrixStats)
library(ggforce)
library(patchwork)
library(ggpubr)
library(cowplot)
library(parallel)Process MOB data from URL
if (!file.exists("output/counts_coords.RData")) {
# data file URL https://www.spatialresearch.org/wp-content/uploads/2016/07/Rep11_MOB_count_matrix-1.tsv
# might take a minute to download
counts_raw = read.delim(url("https://www.spatialresearch.org/wp-content/uploads/2016/07/Rep11_MOB_count_matrix-1.tsv"), header = TRUE, row.names = 1)
# counts_raw = read.delim(file = "Rep11_MOB_count_matrix-1.tsv", header = TRUE, row.names = 1)
dim(counts_raw)
coords_raw = do.call(rbind, strsplit(rownames(counts_raw), "x"))
# xy plane only
coords = apply(coords_raw, 1:2, as.numeric)
colnames(coords) <- c("x","y")
rownames(coords) <- rownames(counts_raw)
plot(coords[,"x"], coords[,"y"])
counts = t(counts_raw)
sce = SingleCellExperiment(assays = list(counts = counts),
colData = coords)
sce <- scater::normalize(sce)
var.fit <- trendVar(sce, parametric=TRUE, loess.args=list(span=0.3), use.spikes = FALSE)
var.out <- decomposeVar(sce, var.fit)
pdf(file = "output/HVG_selection.pdf", height = 8, width = 8)
plot(var.out$mean, var.out$total, pch=16, cex=0.6, xlab="Mean log-expression",
ylab="Variance of log-expression")
curve(var.fit$trend(x), col="dodgerblue", lwd=2, add=TRUE)
seqvals = seq(min(var.out$mean), max(var.out$mean), length.out = 1000)
peakExp = seqvals[which.max(var.fit$trend(seqvals))]
hvg.out <- var.out[which(var.out$FDR <= 0.05 & var.out$mean > peakExp),]
nrow(hvg.out)
hvg.out <- hvg.out[order(hvg.out$bio, decreasing=TRUE),]
points(var.out$mean[which(var.out$FDR <= 0.05 & var.out$mean > peakExp)],
var.out$total[which(var.out$FDR <= 0.05 & var.out$mean > peakExp)], col="red", pch=16)
abline(v = peakExp, lty = 2, col = "black")
dev.off()
head(hvg.out)
HVG = sort(rownames(hvg.out))
expr = logcounts(sce)
save(counts, coords, sce, HVG, expr, file = "output/counts_coords.RData")
} else {
load("output/counts_coords.RData")
}
W = weightMatrix_nD(coords, span = 0.05)Test for spatial differential expression and remove
This takes a long time (a few hours) to run.
#### test for spatial differential expression by using weightedMean
# results in a list of non-spatially DE genes
samepairs = cbind(rownames(expr), rownames(expr))
rownames(samepairs) = samepairs[,1]
DE_stats_all = DCARSacrossNetwork(expr,
samepairs,
W = W,
weightedConcordanceFunction = weightedMeanMatrixStats,
extractTestStatisticOnly = TRUE,
niter = 1000,
verbose = FALSE)
if (!file.exists("output/DE_sampled_permstats.Rdata")) {
# Does globalCor relate to the null distribution for genes?
set.seed(500)
globalMean = rowMeans(expr)
pairs_sampled = samepairs[DCARS::stratifiedSample(globalMean, length = 100),]
sampled_permstats = DCARSacrossNetwork(expr,
pairs_sampled,
W = W,
weightedConcordanceFunction = weightedMeanMatrixStats,
extractPermutationTestStatistics = TRUE,
niter = 1000,
verbose = TRUE)
save(sampled_permstats, pairs_sampled, globalMean, file = "output/DE_sampled_permstats.Rdata")
} else {
load("output/DE_sampled_permstats.Rdata")
}## [1] "Gm10677 Gm10677"
## [1] "extract permuted test statistics"
## [1] "Lhx1 Lhx1"
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## [1] "Itga2b Itga2b"
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## [1] "Stat6 Stat6"
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## [1] "Ankdd1b Ankdd1b"
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## [1] "Casp2 Casp2"
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## [1] "Atf1 Atf1"
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## [1] "Sra1 Sra1"
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## [1] "Brsk1 Brsk1"
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## [1] "X6030419C18Rik X6030419C18Rik"
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## [1] "Smc5 Smc5"
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## [1] "Trappc12 Trappc12"
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## [1] "Bcl11b Bcl11b"
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## [1] "Anapc5 Anapc5"
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## [1] "Gng13 Gng13"
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## [1] "Atp8a1 Atp8a1"
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## [1] "Spin1 Spin1"
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## [1] "Fam174a Fam174a"
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## [1] "Gna11 Gna11"
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## [1] "Akr1a1 Akr1a1"
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## [1] "Ids Ids"
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## [1] "Hsp90b1 Hsp90b1"
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## [1] "Abat Abat"
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## [1] "Tcf4 Tcf4"
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## [1] "Tmsb10 Tmsb10"
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## [1] "Canx Canx"
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## [1] "Aldoc Aldoc"
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## [1] "Marcks Marcks"
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## [1] "Hspa8 Hspa8"
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## [1] "Atp5b Atp5b"
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## [1] "Atp1b1 Atp1b1"
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## [1] "Tmsb4x Tmsb4x"
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## [1] "Calm2 Calm2"
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## [1] "Itm2b Itm2b"
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## [1] "Tuba1a Tuba1a"
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## [1] "Ckb Ckb"
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## [1] "Cpe Cpe"
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## [1] "Sparcl1 Sparcl1"
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## [1] "Actb Actb"
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## [1] "Cst3 Cst3"
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## [1] "Apoe Apoe"
## [1] "extract permuted test statistics"plot(globalMean[rownames(pairs_sampled)], unlist(lapply(unlist(sampled_permstats, recursive = FALSE),quantile, 0.99)))
points(globalMean[rownames(pairs_sampled)], unlist(lapply(unlist(sampled_permstats, recursive = FALSE),quantile, 0.95)), col = "red")
points(globalMean[rownames(pairs_sampled)], unlist(lapply(unlist(sampled_permstats, recursive = FALSE),quantile, 0.90)), col = "blue")
# looks like there is a general relationship between global mean and the null distribution, but this does not appear to be a strong enough association to predict null distribution by just globalMean
# will need to run full permutation testing
if (!file.exists("output/DE_n100_permstats.Rds")) {
set.seed(500)
if (!parallel) {
n100_permstats = DCARSacrossNetwork(expr,
samepairs,
W = W,
weightedConcordanceFunction = weightedMeanMatrixStats,
extractPermutationTestStatistics = TRUE,
niter = 100,
verbose = TRUE)
} else {
split_df = split.data.frame(samepairs, rep(1:ncores, length.out = nrow(samepairs)))
names(split_df) <- NULL
n100_permstats = mclapply(split_df, function(s) {
res = DCARSacrossNetwork(expr,
s,
W = W,
weightedConcordanceFunction = weightedMeanMatrixStats,
extractPermutationTestStatistics = TRUE,
niter = 100,
verbose = TRUE)
res = lapply(res, unlist)
names(res) <- rownames(s)
return(res)
})
n100_permstats = unlist(n100_permstats, recursive = FALSE)
n100_permstats <- n100_permstats[rownames(samepairs)]
}
saveRDS(n100_permstats, file = "output/DE_n100_permstats.Rds")
} else {
n100_permstats = readRDS("output/DE_n100_permstats.Rds")
}
n100_pval = sapply(names(DE_stats_all), function(gene){
mean(unlist(n100_permstats[[gene]]) >= DE_stats_all[gene])
})
# recalculate p-value for those with pval < 0.1 with 1000 iter
# aim is to remove these genes at p-value < 0.05 level
if (!file.exists("output/DE_n1000_pval.Rds")) {
set.seed(500)
if (!parallel) {
n1000_pval = DCARSacrossNetwork(expr,
samepairs[n100_pval < 0.1,],
W = W,
weightedConcordanceFunction = weightedMeanMatrixStats,
niter = 1000,
verbose = TRUE)
} else {
split_df = split.data.frame(samepairs[n100_pval < 0.1,], rep(1:ncores, length.out = nrow(samepairs[n100_pval < 0.1,])))
names(split_df) <- NULL
n1000_pval = mclapply(split_df, function(s) {
res = DCARSacrossNetwork(expr,
s,
W = W,
weightedConcordanceFunction = weightedMeanMatrixStats,
niter = 1000,
verbose = TRUE)
res = lapply(res, unlist)
names(res) <- rownames(s)
return(res)
})
n1000_pval = unlist(n1000_pval)
n1000_pval <- n1000_pval[rownames(samepairs[n100_pval<0.1,])]
}
saveRDS(n1000_pval, file = "output/DE_n1000_pval.Rds")
} else {
n1000_pval = readRDS("output/DE_n1000_pval.Rds")
}
DE_pval = n100_pval
DE_pval[names(n1000_pval)] <- n1000_pval
DE_fdr = p.adjust(DE_pval, method = "BH")
nonDEgenes_fdr = names(which(DE_fdr > 0.05))
saveRDS(nonDEgenes_fdr, file = "output/nonDEgenes_fdr.Rds")
nonDEgenes = names(which(DE_pval > 0.05))
saveRDS(nonDEgenes, file = "output/nonDEgenes.Rds")Perform scHOT spatial correlation testing
pairs = t(combn(intersect(HVG, nonDEgenes),2))
rownames(pairs) <- apply(pairs,1,paste0,collapse = "_")
dim(pairs)## [1] 903 2if (!file.exists("output/sampled_permstats.Rdata")) {
set.seed(500)
# Does globalCor relate to the null distribution for genes?
globalCor = apply(pairs, 1, function(x) cor(counts[x[1],], counts[x[2],], method = "spearman"))
pairs_sampled = pairs[DCARS::stratifiedSample(globalCor, length = 200),]
if (!parallel) {
sampled_permstats = DCARSacrossNetwork(counts,
pairs_sampled,
W = W,
weightedConcordanceFunction = weightedSpearman,
extractPermutationTestStatistics = TRUE,
niter = 1000,
verbose = TRUE)
} else {
split_df = split.data.frame(pairs_sampled, rep(1:ncores, length.out = nrow(pairs_sampled)))
names(split_df) <- NULL
sampled_permstats = mclapply(split_df, function(s) {
res = DCARSacrossNetwork(counts,
s,
W = W,
weightedConcordanceFunction = weightedSpearman,
extractPermutationTestStatistics = TRUE,
niter = 1000,
verbose = TRUE)
res = lapply(res, unlist)
names(res) <- rownames(s)
return(res)
})
sampled_permstats = unlist(sampled_permstats, recursive = FALSE)
sampled_permstats <- sampled_permstats[rownames(pairs_sampled)]
}
save(sampled_permstats, pairs_sampled, globalCor, file = "output/sampled_permstats.Rdata")
} else {
load("output/sampled_permstats.Rdata")
}
permstatsDF = data.frame(
genepair = rep(names(sampled_permstats), times = unlist(lapply(sampled_permstats, function(x) length(unlist(x))))),
stat = unlist(sampled_permstats)
)
permstatsDF$globalCor = globalCor[as.character(permstatsDF$genepair)]
df_99 = data.frame(
genepair = names(sampled_permstats),
globalCor = globalCor[names(sampled_permstats)],
stat_999 = unlist(lapply(sampled_permstats, function(x) quantile(unlist(x), 0.999))),
stat_99 = unlist(lapply(sampled_permstats, function(x) quantile(unlist(x), 0.99))),
stat_95 = unlist(lapply(sampled_permstats, function(x) quantile(unlist(x), 0.95))),
stat_90 = unlist(lapply(sampled_permstats, function(x) quantile(unlist(x), 0.90)))
)
df_99$fitted_999 = loess(stat_999 ~ globalCor, data = df_99)$fitted
df_99$fitted_99 = loess(stat_99 ~ globalCor, data = df_99)$fitted
df_99$fitted_95 = loess(stat_95 ~ globalCor, data = df_99)$fitted
df_99$fitted_90 = loess(stat_90 ~ globalCor, data = df_99)$fitted
g = ggplot(permstatsDF, aes(x = globalCor, y = stat)) +
theme_classic() +
geom_scattermore() +
geom_point(aes(y = stat_999, colour = "0.999"), data = df_99) +
geom_line(aes(y = fitted_999, colour = "0.999"), data = df_99) +
geom_point(aes(y = stat_99, colour = "0.99"), data = df_99) +
geom_line(aes(y = fitted_99, colour = "0.99"), data = df_99) +
geom_point(aes(y = stat_95, colour = "0.95"), data = df_99) +
geom_line(aes(y = fitted_95, colour = "0.95"), data = df_99) +
geom_point(aes(y = stat_90, colour = "0.90"), data = df_99) +
geom_line(aes(y = fitted_90, colour = "0.90"), data = df_99) +
scale_colour_manual(values = c("0.999" = tol12qualitative[4],
"0.99" = tol12qualitative[3],
"0.95" = tol12qualitative[2],
"0.90" = tol12qualitative[1])) +
labs(colour = "Quantile") +
theme(panel.grid = element_blank()) +
xlab("Global Correlation") +
ylab("Permuted test statistics") +
theme(legend.position = "bottom")
g
ggsave(g, file = "output/stats_globalCor_2d.pdf", height = 8, width = 8)
if (!file.exists("output/2D_p_all.Rdata")) {
# estimate the set of p-values
stats_all = DCARSacrossNetwork(counts,
pairs,
W = W,
weightedConcordanceFunction = weightedSpearman,
extractTestStatisticOnly = TRUE,
niter = 1000,
verbose = TRUE)
wcors_all = t(DCARSacrossNetwork(counts,
pairs,
W = W,
weightedConcordanceFunction = weightedSpearman,
extractWcorSequenceOnly = TRUE,
niter = 1000,
verbose = TRUE))
p_all = estimatePvaluesSpearman(stats_all,
globalCor,
sampled_permstats,
usenperm = TRUE,
nperm = 10000,
plot = FALSE,
maxDist = 2,
verbose = TRUE)
p_all$fdr <- p.adjust(p_all$pval, method = "BH")
save(p_all, stats_all, wcors_all, file = "output/2D_p_all.Rdata")
} else {
load("output/2D_p_all.Rdata")
}## [1] "Abat Actb"
## [1] "Abat Arrb1"
## [1] "Abat Atp6v1c1"
## [1] "Abat Atrnl1"
## [1] "Abat Bai1"
## [1] "Abat Calm1"
## [1] "Abat Ccng1"
## [1] "Abat Cldn11"
## [1] "Abat Cnp"
## [1] "Abat Cst3"
## [1] "Abat Dnm1l"
## [1] "Abat Dnm3"
## [1] "Abat Erbb2ip"
## [1] "Abat Fam63b"
## [1] "Abat Gm15421"
## [1] "Abat Gucy1b3"
## [1] "Abat Igf2"
## [1] "Abat Ildr2"
## [1] "Abat Impact"
## [1] "Abat Itm2c"
## [1] "Abat Luzp2"
## [1] "Abat Mlc1"
## [1] "Abat Mtor"
## [1] "Abat Myo10"
## [1] "Abat Nfib"
## [1] "Abat Ntng1"
## [1] "Abat Plekha1"
## [1] "Abat Pmm1"
## [1] "Abat Prrc2b"
## [1] "Abat Prune2"
## [1] "Abat Scd2"
## [1] "Abat Slc1a3"
## [1] "Abat Smim13"
## [1] "Abat Sp8"
## [1] "Abat Tiam1"
## [1] "Abat Tmem47"
## [1] "Abat Tmsb4x"
## [1] "Abat Tuba1a"
## [1] "Abat Uchl1"
## [1] "Abat Utrn"
## [1] "Abat Vdac3"
## [1] "Abat Wdfy3"
## [1] "Actb Arrb1"
## [1] "Actb Atp6v1c1"
## [1] "Actb Atrnl1"
## [1] "Actb Bai1"
## [1] "Actb Calm1"
## [1] "Actb Ccng1"
## [1] "Actb Cldn11"
## [1] "Actb Cnp"
## [1] "Actb Cst3"
## [1] "Actb Dnm1l"
## [1] "Actb Dnm3"
## [1] "Actb Erbb2ip"
## [1] "Actb Fam63b"
## [1] "Actb Gm15421"
## [1] "Actb Gucy1b3"
## [1] "Actb Igf2"
## [1] "Actb Ildr2"
## [1] "Actb Impact"
## [1] "Actb Itm2c"
## [1] "Actb Luzp2"
## [1] "Actb Mlc1"
## [1] "Actb Mtor"
## [1] "Actb Myo10"
## [1] "Actb Nfib"
## [1] "Actb Ntng1"
## [1] "Actb Plekha1"
## [1] "Actb Pmm1"
## [1] "Actb Prrc2b"
## [1] "Actb Prune2"
## [1] "Actb Scd2"
## [1] "Actb Slc1a3"
## [1] "Actb Smim13"
## [1] "Actb Sp8"
## [1] "Actb Tiam1"
## [1] "Actb Tmem47"
## [1] "Actb Tmsb4x"
## [1] "Actb Tuba1a"
## [1] "Actb Uchl1"
## [1] "Actb Utrn"
## [1] "Actb Vdac3"
## [1] "Actb Wdfy3"
## [1] "Arrb1 Atp6v1c1"
## [1] "Arrb1 Atrnl1"
## [1] "Arrb1 Bai1"
## [1] "Arrb1 Calm1"
## [1] "Arrb1 Ccng1"
## [1] "Arrb1 Cldn11"
## [1] "Arrb1 Cnp"
## [1] "Arrb1 Cst3"
## [1] "Arrb1 Dnm1l"
## [1] "Arrb1 Dnm3"
## [1] "Arrb1 Erbb2ip"
## [1] "Arrb1 Fam63b"
## [1] "Arrb1 Gm15421"
## [1] "Arrb1 Gucy1b3"
## [1] "Arrb1 Igf2"
## [1] "Arrb1 Ildr2"
## [1] "Arrb1 Impact"
## [1] "Arrb1 Itm2c"
## [1] "Arrb1 Luzp2"
## [1] "Arrb1 Mlc1"
## [1] "Arrb1 Mtor"
## [1] "Arrb1 Myo10"
## [1] "Arrb1 Nfib"
## [1] "Arrb1 Ntng1"
## [1] "Arrb1 Plekha1"
## [1] "Arrb1 Pmm1"
## [1] "Arrb1 Prrc2b"
## [1] "Arrb1 Prune2"
## [1] "Arrb1 Scd2"
## [1] "Arrb1 Slc1a3"
## [1] "Arrb1 Smim13"
## [1] "Arrb1 Sp8"
## [1] "Arrb1 Tiam1"
## [1] "Arrb1 Tmem47"
## [1] "Arrb1 Tmsb4x"
## [1] "Arrb1 Tuba1a"
## [1] "Arrb1 Uchl1"
## [1] "Arrb1 Utrn"
## [1] "Arrb1 Vdac3"
## [1] "Arrb1 Wdfy3"
## [1] "Atp6v1c1 Atrnl1"
## [1] "Atp6v1c1 Bai1"
## [1] "Atp6v1c1 Calm1"
## [1] "Atp6v1c1 Ccng1"
## [1] "Atp6v1c1 Cldn11"
## [1] "Atp6v1c1 Cnp"
## [1] "Atp6v1c1 Cst3"
## [1] "Atp6v1c1 Dnm1l"
## [1] "Atp6v1c1 Dnm3"
## [1] "Atp6v1c1 Erbb2ip"
## [1] "Atp6v1c1 Fam63b"
## [1] "Atp6v1c1 Gm15421"
## [1] "Atp6v1c1 Gucy1b3"
## [1] "Atp6v1c1 Igf2"
## [1] "Atp6v1c1 Ildr2"
## [1] "Atp6v1c1 Impact"
## [1] "Atp6v1c1 Itm2c"
## [1] "Atp6v1c1 Luzp2"
## [1] "Atp6v1c1 Mlc1"
## [1] "Atp6v1c1 Mtor"
## [1] "Atp6v1c1 Myo10"
## [1] "Atp6v1c1 Nfib"
## [1] "Atp6v1c1 Ntng1"
## [1] "Atp6v1c1 Plekha1"
## [1] "Atp6v1c1 Pmm1"
## [1] "Atp6v1c1 Prrc2b"
## [1] "Atp6v1c1 Prune2"
## [1] "Atp6v1c1 Scd2"
## [1] "Atp6v1c1 Slc1a3"
## [1] "Atp6v1c1 Smim13"
## [1] "Atp6v1c1 Sp8"
## [1] "Atp6v1c1 Tiam1"
## [1] "Atp6v1c1 Tmem47"
## [1] "Atp6v1c1 Tmsb4x"
## [1] "Atp6v1c1 Tuba1a"
## [1] "Atp6v1c1 Uchl1"
## [1] "Atp6v1c1 Utrn"
## [1] "Atp6v1c1 Vdac3"
## [1] "Atp6v1c1 Wdfy3"
## [1] "Atrnl1 Bai1"
## [1] "Atrnl1 Calm1"
## [1] "Atrnl1 Ccng1"
## [1] "Atrnl1 Cldn11"
## [1] "Atrnl1 Cnp"
## [1] "Atrnl1 Cst3"
## [1] "Atrnl1 Dnm1l"
## [1] "Atrnl1 Dnm3"
## [1] "Atrnl1 Erbb2ip"
## [1] "Atrnl1 Fam63b"
## [1] "Atrnl1 Gm15421"
## [1] "Atrnl1 Gucy1b3"
## [1] "Atrnl1 Igf2"
## [1] "Atrnl1 Ildr2"
## [1] "Atrnl1 Impact"
## [1] "Atrnl1 Itm2c"
## [1] "Atrnl1 Luzp2"
## [1] "Atrnl1 Mlc1"
## [1] "Atrnl1 Mtor"
## [1] "Atrnl1 Myo10"
## [1] "Atrnl1 Nfib"
## [1] "Atrnl1 Ntng1"
## [1] "Atrnl1 Plekha1"
## [1] "Atrnl1 Pmm1"
## [1] "Atrnl1 Prrc2b"
## [1] "Atrnl1 Prune2"
## [1] "Atrnl1 Scd2"
## [1] "Atrnl1 Slc1a3"
## [1] "Atrnl1 Smim13"
## [1] "Atrnl1 Sp8"
## [1] "Atrnl1 Tiam1"
## [1] "Atrnl1 Tmem47"
## [1] "Atrnl1 Tmsb4x"
## [1] "Atrnl1 Tuba1a"
## [1] "Atrnl1 Uchl1"
## [1] "Atrnl1 Utrn"
## [1] "Atrnl1 Vdac3"
## [1] "Atrnl1 Wdfy3"
## [1] "Bai1 Calm1"
## [1] "Bai1 Ccng1"
## [1] "Bai1 Cldn11"
## [1] "Bai1 Cnp"
## [1] "Bai1 Cst3"
## [1] "Bai1 Dnm1l"
## [1] "Bai1 Dnm3"
## [1] "Bai1 Erbb2ip"
## [1] "Bai1 Fam63b"
## [1] "Bai1 Gm15421"
## [1] "Bai1 Gucy1b3"
## [1] "Bai1 Igf2"
## [1] "Bai1 Ildr2"
## [1] "Bai1 Impact"
## [1] "Bai1 Itm2c"
## [1] "Bai1 Luzp2"
## [1] "Bai1 Mlc1"
## [1] "Bai1 Mtor"
## [1] "Bai1 Myo10"
## [1] "Bai1 Nfib"
## [1] "Bai1 Ntng1"
## [1] "Bai1 Plekha1"
## [1] "Bai1 Pmm1"
## [1] "Bai1 Prrc2b"
## [1] "Bai1 Prune2"
## [1] "Bai1 Scd2"
## [1] "Bai1 Slc1a3"
## [1] "Bai1 Smim13"
## [1] "Bai1 Sp8"
## [1] "Bai1 Tiam1"
## [1] "Bai1 Tmem47"
## [1] "Bai1 Tmsb4x"
## [1] "Bai1 Tuba1a"
## [1] "Bai1 Uchl1"
## [1] "Bai1 Utrn"
## [1] "Bai1 Vdac3"
## [1] "Bai1 Wdfy3"
## [1] "Calm1 Ccng1"
## [1] "Calm1 Cldn11"
## [1] "Calm1 Cnp"
## [1] "Calm1 Cst3"
## [1] "Calm1 Dnm1l"
## [1] "Calm1 Dnm3"
## [1] "Calm1 Erbb2ip"
## [1] "Calm1 Fam63b"
## [1] "Calm1 Gm15421"
## [1] "Calm1 Gucy1b3"
## [1] "Calm1 Igf2"
## [1] "Calm1 Ildr2"
## [1] "Calm1 Impact"
## [1] "Calm1 Itm2c"
## [1] "Calm1 Luzp2"
## [1] "Calm1 Mlc1"
## [1] "Calm1 Mtor"
## [1] "Calm1 Myo10"
## [1] "Calm1 Nfib"
## [1] "Calm1 Ntng1"
## [1] "Calm1 Plekha1"
## [1] "Calm1 Pmm1"
## [1] "Calm1 Prrc2b"
## [1] "Calm1 Prune2"
## [1] "Calm1 Scd2"
## [1] "Calm1 Slc1a3"
## [1] "Calm1 Smim13"
## [1] "Calm1 Sp8"
## [1] "Calm1 Tiam1"
## [1] "Calm1 Tmem47"
## [1] "Calm1 Tmsb4x"
## [1] "Calm1 Tuba1a"
## [1] "Calm1 Uchl1"
## [1] "Calm1 Utrn"
## [1] "Calm1 Vdac3"
## [1] "Calm1 Wdfy3"
## [1] "Ccng1 Cldn11"
## [1] "Ccng1 Cnp"
## [1] "Ccng1 Cst3"
## [1] "Ccng1 Dnm1l"
## [1] "Ccng1 Dnm3"
## [1] "Ccng1 Erbb2ip"
## [1] "Ccng1 Fam63b"
## [1] "Ccng1 Gm15421"
## [1] "Ccng1 Gucy1b3"
## [1] "Ccng1 Igf2"
## [1] "Ccng1 Ildr2"
## [1] "Ccng1 Impact"
## [1] "Ccng1 Itm2c"
## [1] "Ccng1 Luzp2"
## [1] "Ccng1 Mlc1"
## [1] "Ccng1 Mtor"
## [1] "Ccng1 Myo10"
## [1] "Ccng1 Nfib"
## [1] "Ccng1 Ntng1"
## [1] "Ccng1 Plekha1"
## [1] "Ccng1 Pmm1"
## [1] "Ccng1 Prrc2b"
## [1] "Ccng1 Prune2"
## [1] "Ccng1 Scd2"
## [1] "Ccng1 Slc1a3"
## [1] "Ccng1 Smim13"
## [1] "Ccng1 Sp8"
## [1] "Ccng1 Tiam1"
## [1] "Ccng1 Tmem47"
## [1] "Ccng1 Tmsb4x"
## [1] "Ccng1 Tuba1a"
## [1] "Ccng1 Uchl1"
## [1] "Ccng1 Utrn"
## [1] "Ccng1 Vdac3"
## [1] "Ccng1 Wdfy3"
## [1] "Cldn11 Cnp"
## [1] "Cldn11 Cst3"
## [1] "Cldn11 Dnm1l"
## [1] "Cldn11 Dnm3"
## [1] "Cldn11 Erbb2ip"
## [1] "Cldn11 Fam63b"
## [1] "Cldn11 Gm15421"
## [1] "Cldn11 Gucy1b3"
## [1] "Cldn11 Igf2"
## [1] "Cldn11 Ildr2"
## [1] "Cldn11 Impact"
## [1] "Cldn11 Itm2c"
## [1] "Cldn11 Luzp2"
## [1] "Cldn11 Mlc1"
## [1] "Cldn11 Mtor"
## [1] "Cldn11 Myo10"
## [1] "Cldn11 Nfib"
## [1] "Cldn11 Ntng1"
## [1] "Cldn11 Plekha1"
## [1] "Cldn11 Pmm1"
## [1] "Cldn11 Prrc2b"
## [1] "Cldn11 Prune2"
## [1] "Cldn11 Scd2"
## [1] "Cldn11 Slc1a3"
## [1] "Cldn11 Smim13"
## [1] "Cldn11 Sp8"
## [1] "Cldn11 Tiam1"
## [1] "Cldn11 Tmem47"
## [1] "Cldn11 Tmsb4x"
## [1] "Cldn11 Tuba1a"
## [1] "Cldn11 Uchl1"
## [1] "Cldn11 Utrn"
## [1] "Cldn11 Vdac3"
## [1] "Cldn11 Wdfy3"
## [1] "Cnp Cst3"
## [1] "Cnp Dnm1l"
## [1] "Cnp Dnm3"
## [1] "Cnp Erbb2ip"
## [1] "Cnp Fam63b"
## [1] "Cnp Gm15421"
## [1] "Cnp Gucy1b3"
## [1] "Cnp Igf2"
## [1] "Cnp Ildr2"
## [1] "Cnp Impact"
## [1] "Cnp Itm2c"
## [1] "Cnp Luzp2"
## [1] "Cnp Mlc1"
## [1] "Cnp Mtor"
## [1] "Cnp Myo10"
## [1] "Cnp Nfib"
## [1] "Cnp Ntng1"
## [1] "Cnp Plekha1"
## [1] "Cnp Pmm1"
## [1] "Cnp Prrc2b"
## [1] "Cnp Prune2"
## [1] "Cnp Scd2"
## [1] "Cnp Slc1a3"
## [1] "Cnp Smim13"
## [1] "Cnp Sp8"
## [1] "Cnp Tiam1"
## [1] "Cnp Tmem47"
## [1] "Cnp Tmsb4x"
## [1] "Cnp Tuba1a"
## [1] "Cnp Uchl1"
## [1] "Cnp Utrn"
## [1] "Cnp Vdac3"
## [1] "Cnp Wdfy3"
## [1] "Cst3 Dnm1l"
## [1] "Cst3 Dnm3"
## [1] "Cst3 Erbb2ip"
## [1] "Cst3 Fam63b"
## [1] "Cst3 Gm15421"
## [1] "Cst3 Gucy1b3"
## [1] "Cst3 Igf2"
## [1] "Cst3 Ildr2"
## [1] "Cst3 Impact"
## [1] "Cst3 Itm2c"
## [1] "Cst3 Luzp2"
## [1] "Cst3 Mlc1"
## [1] "Cst3 Mtor"
## [1] "Cst3 Myo10"
## [1] "Cst3 Nfib"
## [1] "Cst3 Ntng1"
## [1] "Cst3 Plekha1"
## [1] "Cst3 Pmm1"
## [1] "Cst3 Prrc2b"
## [1] "Cst3 Prune2"
## [1] "Cst3 Scd2"
## [1] "Cst3 Slc1a3"
## [1] "Cst3 Smim13"
## [1] "Cst3 Sp8"
## [1] "Cst3 Tiam1"
## [1] "Cst3 Tmem47"
## [1] "Cst3 Tmsb4x"
## [1] "Cst3 Tuba1a"
## [1] "Cst3 Uchl1"
## [1] "Cst3 Utrn"
## [1] "Cst3 Vdac3"
## [1] "Cst3 Wdfy3"
## [1] "Dnm1l Dnm3"
## [1] "Dnm1l Erbb2ip"
## [1] "Dnm1l Fam63b"
## [1] "Dnm1l Gm15421"
## [1] "Dnm1l Gucy1b3"
## [1] "Dnm1l Igf2"
## [1] "Dnm1l Ildr2"
## [1] "Dnm1l Impact"
## [1] "Dnm1l Itm2c"
## [1] "Dnm1l Luzp2"
## [1] "Dnm1l Mlc1"
## [1] "Dnm1l Mtor"
## [1] "Dnm1l Myo10"
## [1] "Dnm1l Nfib"
## [1] "Dnm1l Ntng1"
## [1] "Dnm1l Plekha1"
## [1] "Dnm1l Pmm1"
## [1] "Dnm1l Prrc2b"
## [1] "Dnm1l Prune2"
## [1] "Dnm1l Scd2"
## [1] "Dnm1l Slc1a3"
## [1] "Dnm1l Smim13"
## [1] "Dnm1l Sp8"
## [1] "Dnm1l Tiam1"
## [1] "Dnm1l Tmem47"
## [1] "Dnm1l Tmsb4x"
## [1] "Dnm1l Tuba1a"
## [1] "Dnm1l Uchl1"
## [1] "Dnm1l Utrn"
## [1] "Dnm1l Vdac3"
## [1] "Dnm1l Wdfy3"
## [1] "Dnm3 Erbb2ip"
## [1] "Dnm3 Fam63b"
## [1] "Dnm3 Gm15421"
## [1] "Dnm3 Gucy1b3"
## [1] "Dnm3 Igf2"
## [1] "Dnm3 Ildr2"
## [1] "Dnm3 Impact"
## [1] "Dnm3 Itm2c"
## [1] "Dnm3 Luzp2"
## [1] "Dnm3 Mlc1"
## [1] "Dnm3 Mtor"
## [1] "Dnm3 Myo10"
## [1] "Dnm3 Nfib"
## [1] "Dnm3 Ntng1"
## [1] "Dnm3 Plekha1"
## [1] "Dnm3 Pmm1"
## [1] "Dnm3 Prrc2b"
## [1] "Dnm3 Prune2"
## [1] "Dnm3 Scd2"
## [1] "Dnm3 Slc1a3"
## [1] "Dnm3 Smim13"
## [1] "Dnm3 Sp8"
## [1] "Dnm3 Tiam1"
## [1] "Dnm3 Tmem47"
## [1] "Dnm3 Tmsb4x"
## [1] "Dnm3 Tuba1a"
## [1] "Dnm3 Uchl1"
## [1] "Dnm3 Utrn"
## [1] "Dnm3 Vdac3"
## [1] "Dnm3 Wdfy3"
## [1] "Erbb2ip Fam63b"
## [1] "Erbb2ip Gm15421"
## [1] "Erbb2ip Gucy1b3"
## [1] "Erbb2ip Igf2"
## [1] "Erbb2ip Ildr2"
## [1] "Erbb2ip Impact"
## [1] "Erbb2ip Itm2c"
## [1] "Erbb2ip Luzp2"
## [1] "Erbb2ip Mlc1"
## [1] "Erbb2ip Mtor"
## [1] "Erbb2ip Myo10"
## [1] "Erbb2ip Nfib"
## [1] "Erbb2ip Ntng1"
## [1] "Erbb2ip Plekha1"
## [1] "Erbb2ip Pmm1"
## [1] "Erbb2ip Prrc2b"
## [1] "Erbb2ip Prune2"
## [1] "Erbb2ip Scd2"
## [1] "Erbb2ip Slc1a3"
## [1] "Erbb2ip Smim13"
## [1] "Erbb2ip Sp8"
## [1] "Erbb2ip Tiam1"
## [1] "Erbb2ip Tmem47"
## [1] "Erbb2ip Tmsb4x"
## [1] "Erbb2ip Tuba1a"
## [1] "Erbb2ip Uchl1"
## [1] "Erbb2ip Utrn"
## [1] "Erbb2ip Vdac3"
## [1] "Erbb2ip Wdfy3"
## [1] "Fam63b Gm15421"
## [1] "Fam63b Gucy1b3"
## [1] "Fam63b Igf2"
## [1] "Fam63b Ildr2"
## [1] "Fam63b Impact"
## [1] "Fam63b Itm2c"
## [1] "Fam63b Luzp2"
## [1] "Fam63b Mlc1"
## [1] "Fam63b Mtor"
## [1] "Fam63b Myo10"
## [1] "Fam63b Nfib"
## [1] "Fam63b Ntng1"
## [1] "Fam63b Plekha1"
## [1] "Fam63b Pmm1"
## [1] "Fam63b Prrc2b"
## [1] "Fam63b Prune2"
## [1] "Fam63b Scd2"
## [1] "Fam63b Slc1a3"
## [1] "Fam63b Smim13"
## [1] "Fam63b Sp8"
## [1] "Fam63b Tiam1"
## [1] "Fam63b Tmem47"
## [1] "Fam63b Tmsb4x"
## [1] "Fam63b Tuba1a"
## [1] "Fam63b Uchl1"
## [1] "Fam63b Utrn"
## [1] "Fam63b Vdac3"
## [1] "Fam63b Wdfy3"
## [1] "Gm15421 Gucy1b3"
## [1] "Gm15421 Igf2"
## [1] "Gm15421 Ildr2"
## [1] "Gm15421 Impact"
## [1] "Gm15421 Itm2c"
## [1] "Gm15421 Luzp2"
## [1] "Gm15421 Mlc1"
## [1] "Gm15421 Mtor"
## [1] "Gm15421 Myo10"
## [1] "Gm15421 Nfib"
## [1] "Gm15421 Ntng1"
## [1] "Gm15421 Plekha1"
## [1] "Gm15421 Pmm1"
## [1] "Gm15421 Prrc2b"
## [1] "Gm15421 Prune2"
## [1] "Gm15421 Scd2"
## [1] "Gm15421 Slc1a3"
## [1] "Gm15421 Smim13"
## [1] "Gm15421 Sp8"
## [1] "Gm15421 Tiam1"
## [1] "Gm15421 Tmem47"
## [1] "Gm15421 Tmsb4x"
## [1] "Gm15421 Tuba1a"
## [1] "Gm15421 Uchl1"
## [1] "Gm15421 Utrn"
## [1] "Gm15421 Vdac3"
## [1] "Gm15421 Wdfy3"
## [1] "Gucy1b3 Igf2"
## [1] "Gucy1b3 Ildr2"
## [1] "Gucy1b3 Impact"
## [1] "Gucy1b3 Itm2c"
## [1] "Gucy1b3 Luzp2"
## [1] "Gucy1b3 Mlc1"
## [1] "Gucy1b3 Mtor"
## [1] "Gucy1b3 Myo10"
## [1] "Gucy1b3 Nfib"
## [1] "Gucy1b3 Ntng1"
## [1] "Gucy1b3 Plekha1"
## [1] "Gucy1b3 Pmm1"
## [1] "Gucy1b3 Prrc2b"
## [1] "Gucy1b3 Prune2"
## [1] "Gucy1b3 Scd2"
## [1] "Gucy1b3 Slc1a3"
## [1] "Gucy1b3 Smim13"
## [1] "Gucy1b3 Sp8"
## [1] "Gucy1b3 Tiam1"
## [1] "Gucy1b3 Tmem47"
## [1] "Gucy1b3 Tmsb4x"
## [1] "Gucy1b3 Tuba1a"
## [1] "Gucy1b3 Uchl1"
## [1] "Gucy1b3 Utrn"
## [1] "Gucy1b3 Vdac3"
## [1] "Gucy1b3 Wdfy3"
## [1] "Igf2 Ildr2"
## [1] "Igf2 Impact"
## [1] "Igf2 Itm2c"
## [1] "Igf2 Luzp2"
## [1] "Igf2 Mlc1"
## [1] "Igf2 Mtor"
## [1] "Igf2 Myo10"
## [1] "Igf2 Nfib"
## [1] "Igf2 Ntng1"
## [1] "Igf2 Plekha1"
## [1] "Igf2 Pmm1"
## [1] "Igf2 Prrc2b"
## [1] "Igf2 Prune2"
## [1] "Igf2 Scd2"
## [1] "Igf2 Slc1a3"
## [1] "Igf2 Smim13"
## [1] "Igf2 Sp8"
## [1] "Igf2 Tiam1"
## [1] "Igf2 Tmem47"
## [1] "Igf2 Tmsb4x"
## [1] "Igf2 Tuba1a"
## [1] "Igf2 Uchl1"
## [1] "Igf2 Utrn"
## [1] "Igf2 Vdac3"
## [1] "Igf2 Wdfy3"
## [1] "Ildr2 Impact"
## [1] "Ildr2 Itm2c"
## [1] "Ildr2 Luzp2"
## [1] "Ildr2 Mlc1"
## [1] "Ildr2 Mtor"
## [1] "Ildr2 Myo10"
## [1] "Ildr2 Nfib"
## [1] "Ildr2 Ntng1"
## [1] "Ildr2 Plekha1"
## [1] "Ildr2 Pmm1"
## [1] "Ildr2 Prrc2b"
## [1] "Ildr2 Prune2"
## [1] "Ildr2 Scd2"
## [1] "Ildr2 Slc1a3"
## [1] "Ildr2 Smim13"
## [1] "Ildr2 Sp8"
## [1] "Ildr2 Tiam1"
## [1] "Ildr2 Tmem47"
## [1] "Ildr2 Tmsb4x"
## [1] "Ildr2 Tuba1a"
## [1] "Ildr2 Uchl1"
## [1] "Ildr2 Utrn"
## [1] "Ildr2 Vdac3"
## [1] "Ildr2 Wdfy3"
## [1] "Impact Itm2c"
## [1] "Impact Luzp2"
## [1] "Impact Mlc1"
## [1] "Impact Mtor"
## [1] "Impact Myo10"
## [1] "Impact Nfib"
## [1] "Impact Ntng1"
## [1] "Impact Plekha1"
## [1] "Impact Pmm1"
## [1] "Impact Prrc2b"
## [1] "Impact Prune2"
## [1] "Impact Scd2"
## [1] "Impact Slc1a3"
## [1] "Impact Smim13"
## [1] "Impact Sp8"
## [1] "Impact Tiam1"
## [1] "Impact Tmem47"
## [1] "Impact Tmsb4x"
## [1] "Impact Tuba1a"
## [1] "Impact Uchl1"
## [1] "Impact Utrn"
## [1] "Impact Vdac3"
## [1] "Impact Wdfy3"
## [1] "Itm2c Luzp2"
## [1] "Itm2c Mlc1"
## [1] "Itm2c Mtor"
## [1] "Itm2c Myo10"
## [1] "Itm2c Nfib"
## [1] "Itm2c Ntng1"
## [1] "Itm2c Plekha1"
## [1] "Itm2c Pmm1"
## [1] "Itm2c Prrc2b"
## [1] "Itm2c Prune2"
## [1] "Itm2c Scd2"
## [1] "Itm2c Slc1a3"
## [1] "Itm2c Smim13"
## [1] "Itm2c Sp8"
## [1] "Itm2c Tiam1"
## [1] "Itm2c Tmem47"
## [1] "Itm2c Tmsb4x"
## [1] "Itm2c Tuba1a"
## [1] "Itm2c Uchl1"
## [1] "Itm2c Utrn"
## [1] "Itm2c Vdac3"
## [1] "Itm2c Wdfy3"
## [1] "Luzp2 Mlc1"
## [1] "Luzp2 Mtor"
## [1] "Luzp2 Myo10"
## [1] "Luzp2 Nfib"
## [1] "Luzp2 Ntng1"
## [1] "Luzp2 Plekha1"
## [1] "Luzp2 Pmm1"
## [1] "Luzp2 Prrc2b"
## [1] "Luzp2 Prune2"
## [1] "Luzp2 Scd2"
## [1] "Luzp2 Slc1a3"
## [1] "Luzp2 Smim13"
## [1] "Luzp2 Sp8"
## [1] "Luzp2 Tiam1"
## [1] "Luzp2 Tmem47"
## [1] "Luzp2 Tmsb4x"
## [1] "Luzp2 Tuba1a"
## [1] "Luzp2 Uchl1"
## [1] "Luzp2 Utrn"
## [1] "Luzp2 Vdac3"
## [1] "Luzp2 Wdfy3"
## [1] "Mlc1 Mtor"
## [1] "Mlc1 Myo10"
## [1] "Mlc1 Nfib"
## [1] "Mlc1 Ntng1"
## [1] "Mlc1 Plekha1"
## [1] "Mlc1 Pmm1"
## [1] "Mlc1 Prrc2b"
## [1] "Mlc1 Prune2"
## [1] "Mlc1 Scd2"
## [1] "Mlc1 Slc1a3"
## [1] "Mlc1 Smim13"
## [1] "Mlc1 Sp8"
## [1] "Mlc1 Tiam1"
## [1] "Mlc1 Tmem47"
## [1] "Mlc1 Tmsb4x"
## [1] "Mlc1 Tuba1a"
## [1] "Mlc1 Uchl1"
## [1] "Mlc1 Utrn"
## [1] "Mlc1 Vdac3"
## [1] "Mlc1 Wdfy3"
## [1] "Mtor Myo10"
## [1] "Mtor Nfib"
## [1] "Mtor Ntng1"
## [1] "Mtor Plekha1"
## [1] "Mtor Pmm1"
## [1] "Mtor Prrc2b"
## [1] "Mtor Prune2"
## [1] "Mtor Scd2"
## [1] "Mtor Slc1a3"
## [1] "Mtor Smim13"
## [1] "Mtor Sp8"
## [1] "Mtor Tiam1"
## [1] "Mtor Tmem47"
## [1] "Mtor Tmsb4x"
## [1] "Mtor Tuba1a"
## [1] "Mtor Uchl1"
## [1] "Mtor Utrn"
## [1] "Mtor Vdac3"
## [1] "Mtor Wdfy3"
## [1] "Myo10 Nfib"
## [1] "Myo10 Ntng1"
## [1] "Myo10 Plekha1"
## [1] "Myo10 Pmm1"
## [1] "Myo10 Prrc2b"
## [1] "Myo10 Prune2"
## [1] "Myo10 Scd2"
## [1] "Myo10 Slc1a3"
## [1] "Myo10 Smim13"
## [1] "Myo10 Sp8"
## [1] "Myo10 Tiam1"
## [1] "Myo10 Tmem47"
## [1] "Myo10 Tmsb4x"
## [1] "Myo10 Tuba1a"
## [1] "Myo10 Uchl1"
## [1] "Myo10 Utrn"
## [1] "Myo10 Vdac3"
## [1] "Myo10 Wdfy3"
## [1] "Nfib Ntng1"
## [1] "Nfib Plekha1"
## [1] "Nfib Pmm1"
## [1] "Nfib Prrc2b"
## [1] "Nfib Prune2"
## [1] "Nfib Scd2"
## [1] "Nfib Slc1a3"
## [1] "Nfib Smim13"
## [1] "Nfib Sp8"
## [1] "Nfib Tiam1"
## [1] "Nfib Tmem47"
## [1] "Nfib Tmsb4x"
## [1] "Nfib Tuba1a"
## [1] "Nfib Uchl1"
## [1] "Nfib Utrn"
## [1] "Nfib Vdac3"
## [1] "Nfib Wdfy3"
## [1] "Ntng1 Plekha1"
## [1] "Ntng1 Pmm1"
## [1] "Ntng1 Prrc2b"
## [1] "Ntng1 Prune2"
## [1] "Ntng1 Scd2"
## [1] "Ntng1 Slc1a3"
## [1] "Ntng1 Smim13"
## [1] "Ntng1 Sp8"
## [1] "Ntng1 Tiam1"
## [1] "Ntng1 Tmem47"
## [1] "Ntng1 Tmsb4x"
## [1] "Ntng1 Tuba1a"
## [1] "Ntng1 Uchl1"
## [1] "Ntng1 Utrn"
## [1] "Ntng1 Vdac3"
## [1] "Ntng1 Wdfy3"
## [1] "Plekha1 Pmm1"
## [1] "Plekha1 Prrc2b"
## [1] "Plekha1 Prune2"
## [1] "Plekha1 Scd2"
## [1] "Plekha1 Slc1a3"
## [1] "Plekha1 Smim13"
## [1] "Plekha1 Sp8"
## [1] "Plekha1 Tiam1"
## [1] "Plekha1 Tmem47"
## [1] "Plekha1 Tmsb4x"
## [1] "Plekha1 Tuba1a"
## [1] "Plekha1 Uchl1"
## [1] "Plekha1 Utrn"
## [1] "Plekha1 Vdac3"
## [1] "Plekha1 Wdfy3"
## [1] "Pmm1 Prrc2b"
## [1] "Pmm1 Prune2"
## [1] "Pmm1 Scd2"
## [1] "Pmm1 Slc1a3"
## [1] "Pmm1 Smim13"
## [1] "Pmm1 Sp8"
## [1] "Pmm1 Tiam1"
## [1] "Pmm1 Tmem47"
## [1] "Pmm1 Tmsb4x"
## [1] "Pmm1 Tuba1a"
## [1] "Pmm1 Uchl1"
## [1] "Pmm1 Utrn"
## [1] "Pmm1 Vdac3"
## [1] "Pmm1 Wdfy3"
## [1] "Prrc2b Prune2"
## [1] "Prrc2b Scd2"
## [1] "Prrc2b Slc1a3"
## [1] "Prrc2b Smim13"
## [1] "Prrc2b Sp8"
## [1] "Prrc2b Tiam1"
## [1] "Prrc2b Tmem47"
## [1] "Prrc2b Tmsb4x"
## [1] "Prrc2b Tuba1a"
## [1] "Prrc2b Uchl1"
## [1] "Prrc2b Utrn"
## [1] "Prrc2b Vdac3"
## [1] "Prrc2b Wdfy3"
## [1] "Prune2 Scd2"
## [1] "Prune2 Slc1a3"
## [1] "Prune2 Smim13"
## [1] "Prune2 Sp8"
## [1] "Prune2 Tiam1"
## [1] "Prune2 Tmem47"
## [1] "Prune2 Tmsb4x"
## [1] "Prune2 Tuba1a"
## [1] "Prune2 Uchl1"
## [1] "Prune2 Utrn"
## [1] "Prune2 Vdac3"
## [1] "Prune2 Wdfy3"
## [1] "Scd2 Slc1a3"
## [1] "Scd2 Smim13"
## [1] "Scd2 Sp8"
## [1] "Scd2 Tiam1"
## [1] "Scd2 Tmem47"
## [1] "Scd2 Tmsb4x"
## [1] "Scd2 Tuba1a"
## [1] "Scd2 Uchl1"
## [1] "Scd2 Utrn"
## [1] "Scd2 Vdac3"
## [1] "Scd2 Wdfy3"
## [1] "Slc1a3 Smim13"
## [1] "Slc1a3 Sp8"
## [1] "Slc1a3 Tiam1"
## [1] "Slc1a3 Tmem47"
## [1] "Slc1a3 Tmsb4x"
## [1] "Slc1a3 Tuba1a"
## [1] "Slc1a3 Uchl1"
## [1] "Slc1a3 Utrn"
## [1] "Slc1a3 Vdac3"
## [1] "Slc1a3 Wdfy3"
## [1] "Smim13 Sp8"
## [1] "Smim13 Tiam1"
## [1] "Smim13 Tmem47"
## [1] "Smim13 Tmsb4x"
## [1] "Smim13 Tuba1a"
## [1] "Smim13 Uchl1"
## [1] "Smim13 Utrn"
## [1] "Smim13 Vdac3"
## [1] "Smim13 Wdfy3"
## [1] "Sp8 Tiam1"
## [1] "Sp8 Tmem47"
## [1] "Sp8 Tmsb4x"
## [1] "Sp8 Tuba1a"
## [1] "Sp8 Uchl1"
## [1] "Sp8 Utrn"
## [1] "Sp8 Vdac3"
## [1] "Sp8 Wdfy3"
## [1] "Tiam1 Tmem47"
## [1] "Tiam1 Tmsb4x"
## [1] "Tiam1 Tuba1a"
## [1] "Tiam1 Uchl1"
## [1] "Tiam1 Utrn"
## [1] "Tiam1 Vdac3"
## [1] "Tiam1 Wdfy3"
## [1] "Tmem47 Tmsb4x"
## [1] "Tmem47 Tuba1a"
## [1] "Tmem47 Uchl1"
## [1] "Tmem47 Utrn"
## [1] "Tmem47 Vdac3"
## [1] "Tmem47 Wdfy3"
## [1] "Tmsb4x Tuba1a"
## [1] "Tmsb4x Uchl1"
## [1] "Tmsb4x Utrn"
## [1] "Tmsb4x Vdac3"
## [1] "Tmsb4x Wdfy3"
## [1] "Tuba1a Uchl1"
## [1] "Tuba1a Utrn"
## [1] "Tuba1a Vdac3"
## [1] "Tuba1a Wdfy3"
## [1] "Uchl1 Utrn"
## [1] "Uchl1 Vdac3"
## [1] "Uchl1 Wdfy3"
## [1] "Utrn Vdac3"
## [1] "Utrn Wdfy3"
## [1] "Vdac3 Wdfy3"
## [1] "Abat Actb"
## [1] "Abat Arrb1"
## [1] "Abat Atp6v1c1"
## [1] "Abat Atrnl1"
## [1] "Abat Bai1"
## [1] "Abat Calm1"
## [1] "Abat Ccng1"
## [1] "Abat Cldn11"
## [1] "Abat Cnp"
## [1] "Abat Cst3"
## [1] "Abat Dnm1l"
## [1] "Abat Dnm3"
## [1] "Abat Erbb2ip"
## [1] "Abat Fam63b"
## [1] "Abat Gm15421"
## [1] "Abat Gucy1b3"
## [1] "Abat Igf2"
## [1] "Abat Ildr2"
## [1] "Abat Impact"
## [1] "Abat Itm2c"
## [1] "Abat Luzp2"
## [1] "Abat Mlc1"
## [1] "Abat Mtor"
## [1] "Abat Myo10"
## [1] "Abat Nfib"
## [1] "Abat Ntng1"
## [1] "Abat Plekha1"
## [1] "Abat Pmm1"
## [1] "Abat Prrc2b"
## [1] "Abat Prune2"
## [1] "Abat Scd2"
## [1] "Abat Slc1a3"
## [1] "Abat Smim13"
## [1] "Abat Sp8"
## [1] "Abat Tiam1"
## [1] "Abat Tmem47"
## [1] "Abat Tmsb4x"
## [1] "Abat Tuba1a"
## [1] "Abat Uchl1"
## [1] "Abat Utrn"
## [1] "Abat Vdac3"
## [1] "Abat Wdfy3"
## [1] "Actb Arrb1"
## [1] "Actb Atp6v1c1"
## [1] "Actb Atrnl1"
## [1] "Actb Bai1"
## [1] "Actb Calm1"
## [1] "Actb Ccng1"
## [1] "Actb Cldn11"
## [1] "Actb Cnp"
## [1] "Actb Cst3"
## [1] "Actb Dnm1l"
## [1] "Actb Dnm3"
## [1] "Actb Erbb2ip"
## [1] "Actb Fam63b"
## [1] "Actb Gm15421"
## [1] "Actb Gucy1b3"
## [1] "Actb Igf2"
## [1] "Actb Ildr2"
## [1] "Actb Impact"
## [1] "Actb Itm2c"
## [1] "Actb Luzp2"
## [1] "Actb Mlc1"
## [1] "Actb Mtor"
## [1] "Actb Myo10"
## [1] "Actb Nfib"
## [1] "Actb Ntng1"
## [1] "Actb Plekha1"
## [1] "Actb Pmm1"
## [1] "Actb Prrc2b"
## [1] "Actb Prune2"
## [1] "Actb Scd2"
## [1] "Actb Slc1a3"
## [1] "Actb Smim13"
## [1] "Actb Sp8"
## [1] "Actb Tiam1"
## [1] "Actb Tmem47"
## [1] "Actb Tmsb4x"
## [1] "Actb Tuba1a"
## [1] "Actb Uchl1"
## [1] "Actb Utrn"
## [1] "Actb Vdac3"
## [1] "Actb Wdfy3"
## [1] "Arrb1 Atp6v1c1"
## [1] "Arrb1 Atrnl1"
## [1] "Arrb1 Bai1"
## [1] "Arrb1 Calm1"
## [1] "Arrb1 Ccng1"
## [1] "Arrb1 Cldn11"
## [1] "Arrb1 Cnp"
## [1] "Arrb1 Cst3"
## [1] "Arrb1 Dnm1l"
## [1] "Arrb1 Dnm3"
## [1] "Arrb1 Erbb2ip"
## [1] "Arrb1 Fam63b"
## [1] "Arrb1 Gm15421"
## [1] "Arrb1 Gucy1b3"
## [1] "Arrb1 Igf2"
## [1] "Arrb1 Ildr2"
## [1] "Arrb1 Impact"
## [1] "Arrb1 Itm2c"
## [1] "Arrb1 Luzp2"
## [1] "Arrb1 Mlc1"
## [1] "Arrb1 Mtor"
## [1] "Arrb1 Myo10"
## [1] "Arrb1 Nfib"
## [1] "Arrb1 Ntng1"
## [1] "Arrb1 Plekha1"
## [1] "Arrb1 Pmm1"
## [1] "Arrb1 Prrc2b"
## [1] "Arrb1 Prune2"
## [1] "Arrb1 Scd2"
## [1] "Arrb1 Slc1a3"
## [1] "Arrb1 Smim13"
## [1] "Arrb1 Sp8"
## [1] "Arrb1 Tiam1"
## [1] "Arrb1 Tmem47"
## [1] "Arrb1 Tmsb4x"
## [1] "Arrb1 Tuba1a"
## [1] "Arrb1 Uchl1"
## [1] "Arrb1 Utrn"
## [1] "Arrb1 Vdac3"
## [1] "Arrb1 Wdfy3"
## [1] "Atp6v1c1 Atrnl1"
## [1] "Atp6v1c1 Bai1"
## [1] "Atp6v1c1 Calm1"
## [1] "Atp6v1c1 Ccng1"
## [1] "Atp6v1c1 Cldn11"
## [1] "Atp6v1c1 Cnp"
## [1] "Atp6v1c1 Cst3"
## [1] "Atp6v1c1 Dnm1l"
## [1] "Atp6v1c1 Dnm3"
## [1] "Atp6v1c1 Erbb2ip"
## [1] "Atp6v1c1 Fam63b"
## [1] "Atp6v1c1 Gm15421"
## [1] "Atp6v1c1 Gucy1b3"
## [1] "Atp6v1c1 Igf2"
## [1] "Atp6v1c1 Ildr2"
## [1] "Atp6v1c1 Impact"
## [1] "Atp6v1c1 Itm2c"
## [1] "Atp6v1c1 Luzp2"
## [1] "Atp6v1c1 Mlc1"
## [1] "Atp6v1c1 Mtor"
## [1] "Atp6v1c1 Myo10"
## [1] "Atp6v1c1 Nfib"
## [1] "Atp6v1c1 Ntng1"
## [1] "Atp6v1c1 Plekha1"
## [1] "Atp6v1c1 Pmm1"
## [1] "Atp6v1c1 Prrc2b"
## [1] "Atp6v1c1 Prune2"
## [1] "Atp6v1c1 Scd2"
## [1] "Atp6v1c1 Slc1a3"
## [1] "Atp6v1c1 Smim13"
## [1] "Atp6v1c1 Sp8"
## [1] "Atp6v1c1 Tiam1"
## [1] "Atp6v1c1 Tmem47"
## [1] "Atp6v1c1 Tmsb4x"
## [1] "Atp6v1c1 Tuba1a"
## [1] "Atp6v1c1 Uchl1"
## [1] "Atp6v1c1 Utrn"
## [1] "Atp6v1c1 Vdac3"
## [1] "Atp6v1c1 Wdfy3"
## [1] "Atrnl1 Bai1"
## [1] "Atrnl1 Calm1"
## [1] "Atrnl1 Ccng1"
## [1] "Atrnl1 Cldn11"
## [1] "Atrnl1 Cnp"
## [1] "Atrnl1 Cst3"
## [1] "Atrnl1 Dnm1l"
## [1] "Atrnl1 Dnm3"
## [1] "Atrnl1 Erbb2ip"
## [1] "Atrnl1 Fam63b"
## [1] "Atrnl1 Gm15421"
## [1] "Atrnl1 Gucy1b3"
## [1] "Atrnl1 Igf2"
## [1] "Atrnl1 Ildr2"
## [1] "Atrnl1 Impact"
## [1] "Atrnl1 Itm2c"
## [1] "Atrnl1 Luzp2"
## [1] "Atrnl1 Mlc1"
## [1] "Atrnl1 Mtor"
## [1] "Atrnl1 Myo10"
## [1] "Atrnl1 Nfib"
## [1] "Atrnl1 Ntng1"
## [1] "Atrnl1 Plekha1"
## [1] "Atrnl1 Pmm1"
## [1] "Atrnl1 Prrc2b"
## [1] "Atrnl1 Prune2"
## [1] "Atrnl1 Scd2"
## [1] "Atrnl1 Slc1a3"
## [1] "Atrnl1 Smim13"
## [1] "Atrnl1 Sp8"
## [1] "Atrnl1 Tiam1"
## [1] "Atrnl1 Tmem47"
## [1] "Atrnl1 Tmsb4x"
## [1] "Atrnl1 Tuba1a"
## [1] "Atrnl1 Uchl1"
## [1] "Atrnl1 Utrn"
## [1] "Atrnl1 Vdac3"
## [1] "Atrnl1 Wdfy3"
## [1] "Bai1 Calm1"
## [1] "Bai1 Ccng1"
## [1] "Bai1 Cldn11"
## [1] "Bai1 Cnp"
## [1] "Bai1 Cst3"
## [1] "Bai1 Dnm1l"
## [1] "Bai1 Dnm3"
## [1] "Bai1 Erbb2ip"
## [1] "Bai1 Fam63b"
## [1] "Bai1 Gm15421"
## [1] "Bai1 Gucy1b3"
## [1] "Bai1 Igf2"
## [1] "Bai1 Ildr2"
## [1] "Bai1 Impact"
## [1] "Bai1 Itm2c"
## [1] "Bai1 Luzp2"
## [1] "Bai1 Mlc1"
## [1] "Bai1 Mtor"
## [1] "Bai1 Myo10"
## [1] "Bai1 Nfib"
## [1] "Bai1 Ntng1"
## [1] "Bai1 Plekha1"
## [1] "Bai1 Pmm1"
## [1] "Bai1 Prrc2b"
## [1] "Bai1 Prune2"
## [1] "Bai1 Scd2"
## [1] "Bai1 Slc1a3"
## [1] "Bai1 Smim13"
## [1] "Bai1 Sp8"
## [1] "Bai1 Tiam1"
## [1] "Bai1 Tmem47"
## [1] "Bai1 Tmsb4x"
## [1] "Bai1 Tuba1a"
## [1] "Bai1 Uchl1"
## [1] "Bai1 Utrn"
## [1] "Bai1 Vdac3"
## [1] "Bai1 Wdfy3"
## [1] "Calm1 Ccng1"
## [1] "Calm1 Cldn11"
## [1] "Calm1 Cnp"
## [1] "Calm1 Cst3"
## [1] "Calm1 Dnm1l"
## [1] "Calm1 Dnm3"
## [1] "Calm1 Erbb2ip"
## [1] "Calm1 Fam63b"
## [1] "Calm1 Gm15421"
## [1] "Calm1 Gucy1b3"
## [1] "Calm1 Igf2"
## [1] "Calm1 Ildr2"
## [1] "Calm1 Impact"
## [1] "Calm1 Itm2c"
## [1] "Calm1 Luzp2"
## [1] "Calm1 Mlc1"
## [1] "Calm1 Mtor"
## [1] "Calm1 Myo10"
## [1] "Calm1 Nfib"
## [1] "Calm1 Ntng1"
## [1] "Calm1 Plekha1"
## [1] "Calm1 Pmm1"
## [1] "Calm1 Prrc2b"
## [1] "Calm1 Prune2"
## [1] "Calm1 Scd2"
## [1] "Calm1 Slc1a3"
## [1] "Calm1 Smim13"
## [1] "Calm1 Sp8"
## [1] "Calm1 Tiam1"
## [1] "Calm1 Tmem47"
## [1] "Calm1 Tmsb4x"
## [1] "Calm1 Tuba1a"
## [1] "Calm1 Uchl1"
## [1] "Calm1 Utrn"
## [1] "Calm1 Vdac3"
## [1] "Calm1 Wdfy3"
## [1] "Ccng1 Cldn11"
## [1] "Ccng1 Cnp"
## [1] "Ccng1 Cst3"
## [1] "Ccng1 Dnm1l"
## [1] "Ccng1 Dnm3"
## [1] "Ccng1 Erbb2ip"
## [1] "Ccng1 Fam63b"
## [1] "Ccng1 Gm15421"
## [1] "Ccng1 Gucy1b3"
## [1] "Ccng1 Igf2"
## [1] "Ccng1 Ildr2"
## [1] "Ccng1 Impact"
## [1] "Ccng1 Itm2c"
## [1] "Ccng1 Luzp2"
## [1] "Ccng1 Mlc1"
## [1] "Ccng1 Mtor"
## [1] "Ccng1 Myo10"
## [1] "Ccng1 Nfib"
## [1] "Ccng1 Ntng1"
## [1] "Ccng1 Plekha1"
## [1] "Ccng1 Pmm1"
## [1] "Ccng1 Prrc2b"
## [1] "Ccng1 Prune2"
## [1] "Ccng1 Scd2"
## [1] "Ccng1 Slc1a3"
## [1] "Ccng1 Smim13"
## [1] "Ccng1 Sp8"
## [1] "Ccng1 Tiam1"
## [1] "Ccng1 Tmem47"
## [1] "Ccng1 Tmsb4x"
## [1] "Ccng1 Tuba1a"
## [1] "Ccng1 Uchl1"
## [1] "Ccng1 Utrn"
## [1] "Ccng1 Vdac3"
## [1] "Ccng1 Wdfy3"
## [1] "Cldn11 Cnp"
## [1] "Cldn11 Cst3"
## [1] "Cldn11 Dnm1l"
## [1] "Cldn11 Dnm3"
## [1] "Cldn11 Erbb2ip"
## [1] "Cldn11 Fam63b"
## [1] "Cldn11 Gm15421"
## [1] "Cldn11 Gucy1b3"
## [1] "Cldn11 Igf2"
## [1] "Cldn11 Ildr2"
## [1] "Cldn11 Impact"
## [1] "Cldn11 Itm2c"
## [1] "Cldn11 Luzp2"
## [1] "Cldn11 Mlc1"
## [1] "Cldn11 Mtor"
## [1] "Cldn11 Myo10"
## [1] "Cldn11 Nfib"
## [1] "Cldn11 Ntng1"
## [1] "Cldn11 Plekha1"
## [1] "Cldn11 Pmm1"
## [1] "Cldn11 Prrc2b"
## [1] "Cldn11 Prune2"
## [1] "Cldn11 Scd2"
## [1] "Cldn11 Slc1a3"
## [1] "Cldn11 Smim13"
## [1] "Cldn11 Sp8"
## [1] "Cldn11 Tiam1"
## [1] "Cldn11 Tmem47"
## [1] "Cldn11 Tmsb4x"
## [1] "Cldn11 Tuba1a"
## [1] "Cldn11 Uchl1"
## [1] "Cldn11 Utrn"
## [1] "Cldn11 Vdac3"
## [1] "Cldn11 Wdfy3"
## [1] "Cnp Cst3"
## [1] "Cnp Dnm1l"
## [1] "Cnp Dnm3"
## [1] "Cnp Erbb2ip"
## [1] "Cnp Fam63b"
## [1] "Cnp Gm15421"
## [1] "Cnp Gucy1b3"
## [1] "Cnp Igf2"
## [1] "Cnp Ildr2"
## [1] "Cnp Impact"
## [1] "Cnp Itm2c"
## [1] "Cnp Luzp2"
## [1] "Cnp Mlc1"
## [1] "Cnp Mtor"
## [1] "Cnp Myo10"
## [1] "Cnp Nfib"
## [1] "Cnp Ntng1"
## [1] "Cnp Plekha1"
## [1] "Cnp Pmm1"
## [1] "Cnp Prrc2b"
## [1] "Cnp Prune2"
## [1] "Cnp Scd2"
## [1] "Cnp Slc1a3"
## [1] "Cnp Smim13"
## [1] "Cnp Sp8"
## [1] "Cnp Tiam1"
## [1] "Cnp Tmem47"
## [1] "Cnp Tmsb4x"
## [1] "Cnp Tuba1a"
## [1] "Cnp Uchl1"
## [1] "Cnp Utrn"
## [1] "Cnp Vdac3"
## [1] "Cnp Wdfy3"
## [1] "Cst3 Dnm1l"
## [1] "Cst3 Dnm3"
## [1] "Cst3 Erbb2ip"
## [1] "Cst3 Fam63b"
## [1] "Cst3 Gm15421"
## [1] "Cst3 Gucy1b3"
## [1] "Cst3 Igf2"
## [1] "Cst3 Ildr2"
## [1] "Cst3 Impact"
## [1] "Cst3 Itm2c"
## [1] "Cst3 Luzp2"
## [1] "Cst3 Mlc1"
## [1] "Cst3 Mtor"
## [1] "Cst3 Myo10"
## [1] "Cst3 Nfib"
## [1] "Cst3 Ntng1"
## [1] "Cst3 Plekha1"
## [1] "Cst3 Pmm1"
## [1] "Cst3 Prrc2b"
## [1] "Cst3 Prune2"
## [1] "Cst3 Scd2"
## [1] "Cst3 Slc1a3"
## [1] "Cst3 Smim13"
## [1] "Cst3 Sp8"
## [1] "Cst3 Tiam1"
## [1] "Cst3 Tmem47"
## [1] "Cst3 Tmsb4x"
## [1] "Cst3 Tuba1a"
## [1] "Cst3 Uchl1"
## [1] "Cst3 Utrn"
## [1] "Cst3 Vdac3"
## [1] "Cst3 Wdfy3"
## [1] "Dnm1l Dnm3"
## [1] "Dnm1l Erbb2ip"
## [1] "Dnm1l Fam63b"
## [1] "Dnm1l Gm15421"
## [1] "Dnm1l Gucy1b3"
## [1] "Dnm1l Igf2"
## [1] "Dnm1l Ildr2"
## [1] "Dnm1l Impact"
## [1] "Dnm1l Itm2c"
## [1] "Dnm1l Luzp2"
## [1] "Dnm1l Mlc1"
## [1] "Dnm1l Mtor"
## [1] "Dnm1l Myo10"
## [1] "Dnm1l Nfib"
## [1] "Dnm1l Ntng1"
## [1] "Dnm1l Plekha1"
## [1] "Dnm1l Pmm1"
## [1] "Dnm1l Prrc2b"
## [1] "Dnm1l Prune2"
## [1] "Dnm1l Scd2"
## [1] "Dnm1l Slc1a3"
## [1] "Dnm1l Smim13"
## [1] "Dnm1l Sp8"
## [1] "Dnm1l Tiam1"
## [1] "Dnm1l Tmem47"
## [1] "Dnm1l Tmsb4x"
## [1] "Dnm1l Tuba1a"
## [1] "Dnm1l Uchl1"
## [1] "Dnm1l Utrn"
## [1] "Dnm1l Vdac3"
## [1] "Dnm1l Wdfy3"
## [1] "Dnm3 Erbb2ip"
## [1] "Dnm3 Fam63b"
## [1] "Dnm3 Gm15421"
## [1] "Dnm3 Gucy1b3"
## [1] "Dnm3 Igf2"
## [1] "Dnm3 Ildr2"
## [1] "Dnm3 Impact"
## [1] "Dnm3 Itm2c"
## [1] "Dnm3 Luzp2"
## [1] "Dnm3 Mlc1"
## [1] "Dnm3 Mtor"
## [1] "Dnm3 Myo10"
## [1] "Dnm3 Nfib"
## [1] "Dnm3 Ntng1"
## [1] "Dnm3 Plekha1"
## [1] "Dnm3 Pmm1"
## [1] "Dnm3 Prrc2b"
## [1] "Dnm3 Prune2"
## [1] "Dnm3 Scd2"
## [1] "Dnm3 Slc1a3"
## [1] "Dnm3 Smim13"
## [1] "Dnm3 Sp8"
## [1] "Dnm3 Tiam1"
## [1] "Dnm3 Tmem47"
## [1] "Dnm3 Tmsb4x"
## [1] "Dnm3 Tuba1a"
## [1] "Dnm3 Uchl1"
## [1] "Dnm3 Utrn"
## [1] "Dnm3 Vdac3"
## [1] "Dnm3 Wdfy3"
## [1] "Erbb2ip Fam63b"
## [1] "Erbb2ip Gm15421"
## [1] "Erbb2ip Gucy1b3"
## [1] "Erbb2ip Igf2"
## [1] "Erbb2ip Ildr2"
## [1] "Erbb2ip Impact"
## [1] "Erbb2ip Itm2c"
## [1] "Erbb2ip Luzp2"
## [1] "Erbb2ip Mlc1"
## [1] "Erbb2ip Mtor"
## [1] "Erbb2ip Myo10"
## [1] "Erbb2ip Nfib"
## [1] "Erbb2ip Ntng1"
## [1] "Erbb2ip Plekha1"
## [1] "Erbb2ip Pmm1"
## [1] "Erbb2ip Prrc2b"
## [1] "Erbb2ip Prune2"
## [1] "Erbb2ip Scd2"
## [1] "Erbb2ip Slc1a3"
## [1] "Erbb2ip Smim13"
## [1] "Erbb2ip Sp8"
## [1] "Erbb2ip Tiam1"
## [1] "Erbb2ip Tmem47"
## [1] "Erbb2ip Tmsb4x"
## [1] "Erbb2ip Tuba1a"
## [1] "Erbb2ip Uchl1"
## [1] "Erbb2ip Utrn"
## [1] "Erbb2ip Vdac3"
## [1] "Erbb2ip Wdfy3"
## [1] "Fam63b Gm15421"
## [1] "Fam63b Gucy1b3"
## [1] "Fam63b Igf2"
## [1] "Fam63b Ildr2"
## [1] "Fam63b Impact"
## [1] "Fam63b Itm2c"
## [1] "Fam63b Luzp2"
## [1] "Fam63b Mlc1"
## [1] "Fam63b Mtor"
## [1] "Fam63b Myo10"
## [1] "Fam63b Nfib"
## [1] "Fam63b Ntng1"
## [1] "Fam63b Plekha1"
## [1] "Fam63b Pmm1"
## [1] "Fam63b Prrc2b"
## [1] "Fam63b Prune2"
## [1] "Fam63b Scd2"
## [1] "Fam63b Slc1a3"
## [1] "Fam63b Smim13"
## [1] "Fam63b Sp8"
## [1] "Fam63b Tiam1"
## [1] "Fam63b Tmem47"
## [1] "Fam63b Tmsb4x"
## [1] "Fam63b Tuba1a"
## [1] "Fam63b Uchl1"
## [1] "Fam63b Utrn"
## [1] "Fam63b Vdac3"
## [1] "Fam63b Wdfy3"
## [1] "Gm15421 Gucy1b3"
## [1] "Gm15421 Igf2"
## [1] "Gm15421 Ildr2"
## [1] "Gm15421 Impact"
## [1] "Gm15421 Itm2c"
## [1] "Gm15421 Luzp2"
## [1] "Gm15421 Mlc1"
## [1] "Gm15421 Mtor"
## [1] "Gm15421 Myo10"
## [1] "Gm15421 Nfib"
## [1] "Gm15421 Ntng1"
## [1] "Gm15421 Plekha1"
## [1] "Gm15421 Pmm1"
## [1] "Gm15421 Prrc2b"
## [1] "Gm15421 Prune2"
## [1] "Gm15421 Scd2"
## [1] "Gm15421 Slc1a3"
## [1] "Gm15421 Smim13"
## [1] "Gm15421 Sp8"
## [1] "Gm15421 Tiam1"
## [1] "Gm15421 Tmem47"
## [1] "Gm15421 Tmsb4x"
## [1] "Gm15421 Tuba1a"
## [1] "Gm15421 Uchl1"
## [1] "Gm15421 Utrn"
## [1] "Gm15421 Vdac3"
## [1] "Gm15421 Wdfy3"
## [1] "Gucy1b3 Igf2"
## [1] "Gucy1b3 Ildr2"
## [1] "Gucy1b3 Impact"
## [1] "Gucy1b3 Itm2c"
## [1] "Gucy1b3 Luzp2"
## [1] "Gucy1b3 Mlc1"
## [1] "Gucy1b3 Mtor"
## [1] "Gucy1b3 Myo10"
## [1] "Gucy1b3 Nfib"
## [1] "Gucy1b3 Ntng1"
## [1] "Gucy1b3 Plekha1"
## [1] "Gucy1b3 Pmm1"
## [1] "Gucy1b3 Prrc2b"
## [1] "Gucy1b3 Prune2"
## [1] "Gucy1b3 Scd2"
## [1] "Gucy1b3 Slc1a3"
## [1] "Gucy1b3 Smim13"
## [1] "Gucy1b3 Sp8"
## [1] "Gucy1b3 Tiam1"
## [1] "Gucy1b3 Tmem47"
## [1] "Gucy1b3 Tmsb4x"
## [1] "Gucy1b3 Tuba1a"
## [1] "Gucy1b3 Uchl1"
## [1] "Gucy1b3 Utrn"
## [1] "Gucy1b3 Vdac3"
## [1] "Gucy1b3 Wdfy3"
## [1] "Igf2 Ildr2"
## [1] "Igf2 Impact"
## [1] "Igf2 Itm2c"
## [1] "Igf2 Luzp2"
## [1] "Igf2 Mlc1"
## [1] "Igf2 Mtor"
## [1] "Igf2 Myo10"
## [1] "Igf2 Nfib"
## [1] "Igf2 Ntng1"
## [1] "Igf2 Plekha1"
## [1] "Igf2 Pmm1"
## [1] "Igf2 Prrc2b"
## [1] "Igf2 Prune2"
## [1] "Igf2 Scd2"
## [1] "Igf2 Slc1a3"
## [1] "Igf2 Smim13"
## [1] "Igf2 Sp8"
## [1] "Igf2 Tiam1"
## [1] "Igf2 Tmem47"
## [1] "Igf2 Tmsb4x"
## [1] "Igf2 Tuba1a"
## [1] "Igf2 Uchl1"
## [1] "Igf2 Utrn"
## [1] "Igf2 Vdac3"
## [1] "Igf2 Wdfy3"
## [1] "Ildr2 Impact"
## [1] "Ildr2 Itm2c"
## [1] "Ildr2 Luzp2"
## [1] "Ildr2 Mlc1"
## [1] "Ildr2 Mtor"
## [1] "Ildr2 Myo10"
## [1] "Ildr2 Nfib"
## [1] "Ildr2 Ntng1"
## [1] "Ildr2 Plekha1"
## [1] "Ildr2 Pmm1"
## [1] "Ildr2 Prrc2b"
## [1] "Ildr2 Prune2"
## [1] "Ildr2 Scd2"
## [1] "Ildr2 Slc1a3"
## [1] "Ildr2 Smim13"
## [1] "Ildr2 Sp8"
## [1] "Ildr2 Tiam1"
## [1] "Ildr2 Tmem47"
## [1] "Ildr2 Tmsb4x"
## [1] "Ildr2 Tuba1a"
## [1] "Ildr2 Uchl1"
## [1] "Ildr2 Utrn"
## [1] "Ildr2 Vdac3"
## [1] "Ildr2 Wdfy3"
## [1] "Impact Itm2c"
## [1] "Impact Luzp2"
## [1] "Impact Mlc1"
## [1] "Impact Mtor"
## [1] "Impact Myo10"
## [1] "Impact Nfib"
## [1] "Impact Ntng1"
## [1] "Impact Plekha1"
## [1] "Impact Pmm1"
## [1] "Impact Prrc2b"
## [1] "Impact Prune2"
## [1] "Impact Scd2"
## [1] "Impact Slc1a3"
## [1] "Impact Smim13"
## [1] "Impact Sp8"
## [1] "Impact Tiam1"
## [1] "Impact Tmem47"
## [1] "Impact Tmsb4x"
## [1] "Impact Tuba1a"
## [1] "Impact Uchl1"
## [1] "Impact Utrn"
## [1] "Impact Vdac3"
## [1] "Impact Wdfy3"
## [1] "Itm2c Luzp2"
## [1] "Itm2c Mlc1"
## [1] "Itm2c Mtor"
## [1] "Itm2c Myo10"
## [1] "Itm2c Nfib"
## [1] "Itm2c Ntng1"
## [1] "Itm2c Plekha1"
## [1] "Itm2c Pmm1"
## [1] "Itm2c Prrc2b"
## [1] "Itm2c Prune2"
## [1] "Itm2c Scd2"
## [1] "Itm2c Slc1a3"
## [1] "Itm2c Smim13"
## [1] "Itm2c Sp8"
## [1] "Itm2c Tiam1"
## [1] "Itm2c Tmem47"
## [1] "Itm2c Tmsb4x"
## [1] "Itm2c Tuba1a"
## [1] "Itm2c Uchl1"
## [1] "Itm2c Utrn"
## [1] "Itm2c Vdac3"
## [1] "Itm2c Wdfy3"
## [1] "Luzp2 Mlc1"
## [1] "Luzp2 Mtor"
## [1] "Luzp2 Myo10"
## [1] "Luzp2 Nfib"
## [1] "Luzp2 Ntng1"
## [1] "Luzp2 Plekha1"
## [1] "Luzp2 Pmm1"
## [1] "Luzp2 Prrc2b"
## [1] "Luzp2 Prune2"
## [1] "Luzp2 Scd2"
## [1] "Luzp2 Slc1a3"
## [1] "Luzp2 Smim13"
## [1] "Luzp2 Sp8"
## [1] "Luzp2 Tiam1"
## [1] "Luzp2 Tmem47"
## [1] "Luzp2 Tmsb4x"
## [1] "Luzp2 Tuba1a"
## [1] "Luzp2 Uchl1"
## [1] "Luzp2 Utrn"
## [1] "Luzp2 Vdac3"
## [1] "Luzp2 Wdfy3"
## [1] "Mlc1 Mtor"
## [1] "Mlc1 Myo10"
## [1] "Mlc1 Nfib"
## [1] "Mlc1 Ntng1"
## [1] "Mlc1 Plekha1"
## [1] "Mlc1 Pmm1"
## [1] "Mlc1 Prrc2b"
## [1] "Mlc1 Prune2"
## [1] "Mlc1 Scd2"
## [1] "Mlc1 Slc1a3"
## [1] "Mlc1 Smim13"
## [1] "Mlc1 Sp8"
## [1] "Mlc1 Tiam1"
## [1] "Mlc1 Tmem47"
## [1] "Mlc1 Tmsb4x"
## [1] "Mlc1 Tuba1a"
## [1] "Mlc1 Uchl1"
## [1] "Mlc1 Utrn"
## [1] "Mlc1 Vdac3"
## [1] "Mlc1 Wdfy3"
## [1] "Mtor Myo10"
## [1] "Mtor Nfib"
## [1] "Mtor Ntng1"
## [1] "Mtor Plekha1"
## [1] "Mtor Pmm1"
## [1] "Mtor Prrc2b"
## [1] "Mtor Prune2"
## [1] "Mtor Scd2"
## [1] "Mtor Slc1a3"
## [1] "Mtor Smim13"
## [1] "Mtor Sp8"
## [1] "Mtor Tiam1"
## [1] "Mtor Tmem47"
## [1] "Mtor Tmsb4x"
## [1] "Mtor Tuba1a"
## [1] "Mtor Uchl1"
## [1] "Mtor Utrn"
## [1] "Mtor Vdac3"
## [1] "Mtor Wdfy3"
## [1] "Myo10 Nfib"
## [1] "Myo10 Ntng1"
## [1] "Myo10 Plekha1"
## [1] "Myo10 Pmm1"
## [1] "Myo10 Prrc2b"
## [1] "Myo10 Prune2"
## [1] "Myo10 Scd2"
## [1] "Myo10 Slc1a3"
## [1] "Myo10 Smim13"
## [1] "Myo10 Sp8"
## [1] "Myo10 Tiam1"
## [1] "Myo10 Tmem47"
## [1] "Myo10 Tmsb4x"
## [1] "Myo10 Tuba1a"
## [1] "Myo10 Uchl1"
## [1] "Myo10 Utrn"
## [1] "Myo10 Vdac3"
## [1] "Myo10 Wdfy3"
## [1] "Nfib Ntng1"
## [1] "Nfib Plekha1"
## [1] "Nfib Pmm1"
## [1] "Nfib Prrc2b"
## [1] "Nfib Prune2"
## [1] "Nfib Scd2"
## [1] "Nfib Slc1a3"
## [1] "Nfib Smim13"
## [1] "Nfib Sp8"
## [1] "Nfib Tiam1"
## [1] "Nfib Tmem47"
## [1] "Nfib Tmsb4x"
## [1] "Nfib Tuba1a"
## [1] "Nfib Uchl1"
## [1] "Nfib Utrn"
## [1] "Nfib Vdac3"
## [1] "Nfib Wdfy3"
## [1] "Ntng1 Plekha1"
## [1] "Ntng1 Pmm1"
## [1] "Ntng1 Prrc2b"
## [1] "Ntng1 Prune2"
## [1] "Ntng1 Scd2"
## [1] "Ntng1 Slc1a3"
## [1] "Ntng1 Smim13"
## [1] "Ntng1 Sp8"
## [1] "Ntng1 Tiam1"
## [1] "Ntng1 Tmem47"
## [1] "Ntng1 Tmsb4x"
## [1] "Ntng1 Tuba1a"
## [1] "Ntng1 Uchl1"
## [1] "Ntng1 Utrn"
## [1] "Ntng1 Vdac3"
## [1] "Ntng1 Wdfy3"
## [1] "Plekha1 Pmm1"
## [1] "Plekha1 Prrc2b"
## [1] "Plekha1 Prune2"
## [1] "Plekha1 Scd2"
## [1] "Plekha1 Slc1a3"
## [1] "Plekha1 Smim13"
## [1] "Plekha1 Sp8"
## [1] "Plekha1 Tiam1"
## [1] "Plekha1 Tmem47"
## [1] "Plekha1 Tmsb4x"
## [1] "Plekha1 Tuba1a"
## [1] "Plekha1 Uchl1"
## [1] "Plekha1 Utrn"
## [1] "Plekha1 Vdac3"
## [1] "Plekha1 Wdfy3"
## [1] "Pmm1 Prrc2b"
## [1] "Pmm1 Prune2"
## [1] "Pmm1 Scd2"
## [1] "Pmm1 Slc1a3"
## [1] "Pmm1 Smim13"
## [1] "Pmm1 Sp8"
## [1] "Pmm1 Tiam1"
## [1] "Pmm1 Tmem47"
## [1] "Pmm1 Tmsb4x"
## [1] "Pmm1 Tuba1a"
## [1] "Pmm1 Uchl1"
## [1] "Pmm1 Utrn"
## [1] "Pmm1 Vdac3"
## [1] "Pmm1 Wdfy3"
## [1] "Prrc2b Prune2"
## [1] "Prrc2b Scd2"
## [1] "Prrc2b Slc1a3"
## [1] "Prrc2b Smim13"
## [1] "Prrc2b Sp8"
## [1] "Prrc2b Tiam1"
## [1] "Prrc2b Tmem47"
## [1] "Prrc2b Tmsb4x"
## [1] "Prrc2b Tuba1a"
## [1] "Prrc2b Uchl1"
## [1] "Prrc2b Utrn"
## [1] "Prrc2b Vdac3"
## [1] "Prrc2b Wdfy3"
## [1] "Prune2 Scd2"
## [1] "Prune2 Slc1a3"
## [1] "Prune2 Smim13"
## [1] "Prune2 Sp8"
## [1] "Prune2 Tiam1"
## [1] "Prune2 Tmem47"
## [1] "Prune2 Tmsb4x"
## [1] "Prune2 Tuba1a"
## [1] "Prune2 Uchl1"
## [1] "Prune2 Utrn"
## [1] "Prune2 Vdac3"
## [1] "Prune2 Wdfy3"
## [1] "Scd2 Slc1a3"
## [1] "Scd2 Smim13"
## [1] "Scd2 Sp8"
## [1] "Scd2 Tiam1"
## [1] "Scd2 Tmem47"
## [1] "Scd2 Tmsb4x"
## [1] "Scd2 Tuba1a"
## [1] "Scd2 Uchl1"
## [1] "Scd2 Utrn"
## [1] "Scd2 Vdac3"
## [1] "Scd2 Wdfy3"
## [1] "Slc1a3 Smim13"
## [1] "Slc1a3 Sp8"
## [1] "Slc1a3 Tiam1"
## [1] "Slc1a3 Tmem47"
## [1] "Slc1a3 Tmsb4x"
## [1] "Slc1a3 Tuba1a"
## [1] "Slc1a3 Uchl1"
## [1] "Slc1a3 Utrn"
## [1] "Slc1a3 Vdac3"
## [1] "Slc1a3 Wdfy3"
## [1] "Smim13 Sp8"
## [1] "Smim13 Tiam1"
## [1] "Smim13 Tmem47"
## [1] "Smim13 Tmsb4x"
## [1] "Smim13 Tuba1a"
## [1] "Smim13 Uchl1"
## [1] "Smim13 Utrn"
## [1] "Smim13 Vdac3"
## [1] "Smim13 Wdfy3"
## [1] "Sp8 Tiam1"
## [1] "Sp8 Tmem47"
## [1] "Sp8 Tmsb4x"
## [1] "Sp8 Tuba1a"
## [1] "Sp8 Uchl1"
## [1] "Sp8 Utrn"
## [1] "Sp8 Vdac3"
## [1] "Sp8 Wdfy3"
## [1] "Tiam1 Tmem47"
## [1] "Tiam1 Tmsb4x"
## [1] "Tiam1 Tuba1a"
## [1] "Tiam1 Uchl1"
## [1] "Tiam1 Utrn"
## [1] "Tiam1 Vdac3"
## [1] "Tiam1 Wdfy3"
## [1] "Tmem47 Tmsb4x"
## [1] "Tmem47 Tuba1a"
## [1] "Tmem47 Uchl1"
## [1] "Tmem47 Utrn"
## [1] "Tmem47 Vdac3"
## [1] "Tmem47 Wdfy3"
## [1] "Tmsb4x Tuba1a"
## [1] "Tmsb4x Uchl1"
## [1] "Tmsb4x Utrn"
## [1] "Tmsb4x Vdac3"
## [1] "Tmsb4x Wdfy3"
## [1] "Tuba1a Uchl1"
## [1] "Tuba1a Utrn"
## [1] "Tuba1a Vdac3"
## [1] "Tuba1a Wdfy3"
## [1] "Uchl1 Utrn"
## [1] "Uchl1 Vdac3"
## [1] "Uchl1 Wdfy3"
## [1] "Utrn Vdac3"
## [1] "Utrn Wdfy3"
## [1] "Vdac3 Wdfy3"
## [1] "Abat_Actb"
## [1] "Abat_Arrb1"
## [1] "Abat_Atp6v1c1"
## [1] "Abat_Atrnl1"
## [1] "Abat_Bai1"
## [1] "Abat_Calm1"
## [1] "Abat_Ccng1"
## [1] "Abat_Cldn11"
## [1] "Abat_Cnp"
## [1] "Abat_Cst3"
## [1] "Abat_Dnm1l"
## [1] "Abat_Dnm3"
## [1] "Abat_Erbb2ip"
## [1] "Abat_Fam63b"
## [1] "Abat_Gm15421"
## [1] "Abat_Gucy1b3"
## [1] "Abat_Igf2"
## [1] "Abat_Ildr2"
## [1] "Abat_Impact"
## [1] "Abat_Itm2c"
## [1] "Abat_Luzp2"
## [1] "Abat_Mlc1"
## [1] "Abat_Mtor"
## [1] "Abat_Myo10"
## [1] "Abat_Nfib"
## [1] "Abat_Ntng1"
## [1] "Abat_Plekha1"
## [1] "Abat_Pmm1"
## [1] "Abat_Prrc2b"
## [1] "Abat_Prune2"
## [1] "Abat_Scd2"
## [1] "Abat_Slc1a3"
## [1] "Abat_Smim13"
## [1] "Abat_Sp8"
## [1] "Abat_Tiam1"
## [1] "Abat_Tmem47"
## [1] "Abat_Tmsb4x"
## [1] "Abat_Tuba1a"
## [1] "Abat_Uchl1"
## [1] "Abat_Utrn"
## [1] "Abat_Vdac3"
## [1] "Abat_Wdfy3"
## [1] "Actb_Arrb1"
## [1] "Actb_Atp6v1c1"
## [1] "Actb_Atrnl1"
## [1] "Actb_Bai1"
## [1] "Actb_Calm1"
## [1] "Actb_Ccng1"
## [1] "Actb_Cldn11"
## [1] "Actb_Cnp"
## [1] "Actb_Cst3"
## [1] "Actb_Dnm1l"
## [1] "Actb_Dnm3"
## [1] "Actb_Erbb2ip"
## [1] "Actb_Fam63b"
## [1] "Actb_Gm15421"
## [1] "Actb_Gucy1b3"
## [1] "Actb_Igf2"
## [1] "Actb_Ildr2"
## [1] "Actb_Impact"
## [1] "Actb_Itm2c"
## [1] "Actb_Luzp2"
## [1] "Actb_Mlc1"
## [1] "Actb_Mtor"
## [1] "Actb_Myo10"
## [1] "Actb_Nfib"
## [1] "Actb_Ntng1"
## [1] "Actb_Plekha1"
## [1] "Actb_Pmm1"
## [1] "Actb_Prrc2b"
## [1] "Actb_Prune2"
## [1] "Actb_Scd2"
## [1] "Actb_Slc1a3"
## [1] "Actb_Smim13"
## [1] "Actb_Sp8"
## [1] "Actb_Tiam1"
## [1] "Actb_Tmem47"
## [1] "Actb_Tmsb4x"
## [1] "Actb_Tuba1a"
## [1] "Actb_Uchl1"
## [1] "Actb_Utrn"
## [1] "Actb_Vdac3"
## [1] "Actb_Wdfy3"
## [1] "Arrb1_Atp6v1c1"
## [1] "Arrb1_Atrnl1"
## [1] "Arrb1_Bai1"
## [1] "Arrb1_Calm1"
## [1] "Arrb1_Ccng1"
## [1] "Arrb1_Cldn11"
## [1] "Arrb1_Cnp"
## [1] "Arrb1_Cst3"
## [1] "Arrb1_Dnm1l"
## [1] "Arrb1_Dnm3"
## [1] "Arrb1_Erbb2ip"
## [1] "Arrb1_Fam63b"
## [1] "Arrb1_Gm15421"
## [1] "Arrb1_Gucy1b3"
## [1] "Arrb1_Igf2"
## [1] "Arrb1_Ildr2"
## [1] "Arrb1_Impact"
## [1] "Arrb1_Itm2c"
## [1] "Arrb1_Luzp2"
## [1] "Arrb1_Mlc1"
## [1] "Arrb1_Mtor"
## [1] "Arrb1_Myo10"
## [1] "Arrb1_Nfib"
## [1] "Arrb1_Ntng1"
## [1] "Arrb1_Plekha1"
## [1] "Arrb1_Pmm1"
## [1] "Arrb1_Prrc2b"
## [1] "Arrb1_Prune2"
## [1] "Arrb1_Scd2"
## [1] "Arrb1_Slc1a3"
## [1] "Arrb1_Smim13"
## [1] "Arrb1_Sp8"
## [1] "Arrb1_Tiam1"
## [1] "Arrb1_Tmem47"
## [1] "Arrb1_Tmsb4x"
## [1] "Arrb1_Tuba1a"
## [1] "Arrb1_Uchl1"
## [1] "Arrb1_Utrn"
## [1] "Arrb1_Vdac3"
## [1] "Arrb1_Wdfy3"
## [1] "Atp6v1c1_Atrnl1"
## [1] "Atp6v1c1_Bai1"
## [1] "Atp6v1c1_Calm1"
## [1] "Atp6v1c1_Ccng1"
## [1] "Atp6v1c1_Cldn11"
## [1] "Atp6v1c1_Cnp"
## [1] "Atp6v1c1_Cst3"
## [1] "Atp6v1c1_Dnm1l"
## [1] "Atp6v1c1_Dnm3"
## [1] "Atp6v1c1_Erbb2ip"
## [1] "Atp6v1c1_Fam63b"
## [1] "Atp6v1c1_Gm15421"
## [1] "Atp6v1c1_Gucy1b3"
## [1] "Atp6v1c1_Igf2"
## [1] "Atp6v1c1_Ildr2"
## [1] "Atp6v1c1_Impact"
## [1] "Atp6v1c1_Itm2c"
## [1] "Atp6v1c1_Luzp2"
## [1] "Atp6v1c1_Mlc1"
## [1] "Atp6v1c1_Mtor"
## [1] "Atp6v1c1_Myo10"
## [1] "Atp6v1c1_Nfib"
## [1] "Atp6v1c1_Ntng1"
## [1] "Atp6v1c1_Plekha1"
## [1] "Atp6v1c1_Pmm1"
## [1] "Atp6v1c1_Prrc2b"
## [1] "Atp6v1c1_Prune2"
## [1] "Atp6v1c1_Scd2"
## [1] "Atp6v1c1_Slc1a3"
## [1] "Atp6v1c1_Smim13"
## [1] "Atp6v1c1_Sp8"
## [1] "Atp6v1c1_Tiam1"
## [1] "Atp6v1c1_Tmem47"
## [1] "Atp6v1c1_Tmsb4x"
## [1] "Atp6v1c1_Tuba1a"
## [1] "Atp6v1c1_Uchl1"
## [1] "Atp6v1c1_Utrn"
## [1] "Atp6v1c1_Vdac3"
## [1] "Atp6v1c1_Wdfy3"
## [1] "Atrnl1_Bai1"
## [1] "Atrnl1_Calm1"
## [1] "Atrnl1_Ccng1"
## [1] "Atrnl1_Cldn11"
## [1] "Atrnl1_Cnp"
## [1] "Atrnl1_Cst3"
## [1] "Atrnl1_Dnm1l"
## [1] "Atrnl1_Dnm3"
## [1] "Atrnl1_Erbb2ip"
## [1] "Atrnl1_Fam63b"
## [1] "Atrnl1_Gm15421"
## [1] "Atrnl1_Gucy1b3"
## [1] "Atrnl1_Igf2"
## [1] "Atrnl1_Ildr2"
## [1] "Atrnl1_Impact"
## [1] "Atrnl1_Itm2c"
## [1] "Atrnl1_Luzp2"
## [1] "Atrnl1_Mlc1"
## [1] "Atrnl1_Mtor"
## [1] "Atrnl1_Myo10"
## [1] "Atrnl1_Nfib"
## [1] "Atrnl1_Ntng1"
## [1] "Atrnl1_Plekha1"
## [1] "Atrnl1_Pmm1"
## [1] "Atrnl1_Prrc2b"
## [1] "Atrnl1_Prune2"
## [1] "Atrnl1_Scd2"
## [1] "Atrnl1_Slc1a3"
## [1] "Atrnl1_Smim13"
## [1] "Atrnl1_Sp8"
## [1] "Atrnl1_Tiam1"
## [1] "Atrnl1_Tmem47"
## [1] "Atrnl1_Tmsb4x"
## [1] "Atrnl1_Tuba1a"
## [1] "Atrnl1_Uchl1"
## [1] "Atrnl1_Utrn"
## [1] "Atrnl1_Vdac3"
## [1] "Atrnl1_Wdfy3"
## [1] "Bai1_Calm1"
## [1] "Bai1_Ccng1"
## [1] "Bai1_Cldn11"
## [1] "Bai1_Cnp"
## [1] "Bai1_Cst3"
## [1] "Bai1_Dnm1l"
## [1] "Bai1_Dnm3"
## [1] "Bai1_Erbb2ip"
## [1] "Bai1_Fam63b"
## [1] "Bai1_Gm15421"
## [1] "Bai1_Gucy1b3"
## [1] "Bai1_Igf2"
## [1] "Bai1_Ildr2"
## [1] "Bai1_Impact"
## [1] "Bai1_Itm2c"
## [1] "Bai1_Luzp2"
## [1] "Bai1_Mlc1"
## [1] "Bai1_Mtor"
## [1] "Bai1_Myo10"
## [1] "Bai1_Nfib"
## [1] "Bai1_Ntng1"
## [1] "Bai1_Plekha1"
## [1] "Bai1_Pmm1"
## [1] "Bai1_Prrc2b"
## [1] "Bai1_Prune2"
## [1] "Bai1_Scd2"
## [1] "Bai1_Slc1a3"
## [1] "Bai1_Smim13"
## [1] "Bai1_Sp8"
## [1] "Bai1_Tiam1"
## [1] "Bai1_Tmem47"
## [1] "Bai1_Tmsb4x"
## [1] "Bai1_Tuba1a"
## [1] "Bai1_Uchl1"
## [1] "Bai1_Utrn"
## [1] "Bai1_Vdac3"
## [1] "Bai1_Wdfy3"
## [1] "Calm1_Ccng1"
## [1] "Calm1_Cldn11"
## [1] "Calm1_Cnp"
## [1] "Calm1_Cst3"
## [1] "Calm1_Dnm1l"
## [1] "Calm1_Dnm3"
## [1] "Calm1_Erbb2ip"
## [1] "Calm1_Fam63b"
## [1] "Calm1_Gm15421"
## [1] "Calm1_Gucy1b3"
## [1] "Calm1_Igf2"
## [1] "Calm1_Ildr2"
## [1] "Calm1_Impact"
## [1] "Calm1_Itm2c"
## [1] "Calm1_Luzp2"
## [1] "Calm1_Mlc1"
## [1] "Calm1_Mtor"
## [1] "Calm1_Myo10"
## [1] "Calm1_Nfib"
## [1] "Calm1_Ntng1"
## [1] "Calm1_Plekha1"
## [1] "Calm1_Pmm1"
## [1] "Calm1_Prrc2b"
## [1] "Calm1_Prune2"
## [1] "Calm1_Scd2"
## [1] "Calm1_Slc1a3"
## [1] "Calm1_Smim13"
## [1] "Calm1_Sp8"
## [1] "Calm1_Tiam1"
## [1] "Calm1_Tmem47"
## [1] "Calm1_Tmsb4x"
## [1] "Calm1_Tuba1a"
## [1] "Calm1_Uchl1"
## [1] "Calm1_Utrn"
## [1] "Calm1_Vdac3"
## [1] "Calm1_Wdfy3"
## [1] "Ccng1_Cldn11"
## [1] "Ccng1_Cnp"
## [1] "Ccng1_Cst3"
## [1] "Ccng1_Dnm1l"
## [1] "Ccng1_Dnm3"
## [1] "Ccng1_Erbb2ip"
## [1] "Ccng1_Fam63b"
## [1] "Ccng1_Gm15421"
## [1] "Ccng1_Gucy1b3"
## [1] "Ccng1_Igf2"
## [1] "Ccng1_Ildr2"
## [1] "Ccng1_Impact"
## [1] "Ccng1_Itm2c"
## [1] "Ccng1_Luzp2"
## [1] "Ccng1_Mlc1"
## [1] "Ccng1_Mtor"
## [1] "Ccng1_Myo10"
## [1] "Ccng1_Nfib"
## [1] "Ccng1_Ntng1"
## [1] "Ccng1_Plekha1"
## [1] "Ccng1_Pmm1"
## [1] "Ccng1_Prrc2b"
## [1] "Ccng1_Prune2"
## [1] "Ccng1_Scd2"
## [1] "Ccng1_Slc1a3"
## [1] "Ccng1_Smim13"
## [1] "Ccng1_Sp8"
## [1] "Ccng1_Tiam1"
## [1] "Ccng1_Tmem47"
## [1] "Ccng1_Tmsb4x"
## [1] "Ccng1_Tuba1a"
## [1] "Ccng1_Uchl1"
## [1] "Ccng1_Utrn"
## [1] "Ccng1_Vdac3"
## [1] "Ccng1_Wdfy3"
## [1] "Cldn11_Cnp"
## [1] "Cldn11_Cst3"
## [1] "Cldn11_Dnm1l"
## [1] "Cldn11_Dnm3"
## [1] "Cldn11_Erbb2ip"
## [1] "Cldn11_Fam63b"
## [1] "Cldn11_Gm15421"
## [1] "Cldn11_Gucy1b3"
## [1] "Cldn11_Igf2"
## [1] "Cldn11_Ildr2"
## [1] "Cldn11_Impact"
## [1] "Cldn11_Itm2c"
## [1] "Cldn11_Luzp2"
## [1] "Cldn11_Mlc1"
## [1] "Cldn11_Mtor"
## [1] "Cldn11_Myo10"
## [1] "Cldn11_Nfib"
## [1] "Cldn11_Ntng1"
## [1] "Cldn11_Plekha1"
## [1] "Cldn11_Pmm1"
## [1] "Cldn11_Prrc2b"
## [1] "Cldn11_Prune2"
## [1] "Cldn11_Scd2"
## [1] "Cldn11_Slc1a3"
## [1] "Cldn11_Smim13"
## [1] "Cldn11_Sp8"
## [1] "Cldn11_Tiam1"
## [1] "Cldn11_Tmem47"
## [1] "Cldn11_Tmsb4x"
## [1] "Cldn11_Tuba1a"
## [1] "Cldn11_Uchl1"
## [1] "Cldn11_Utrn"
## [1] "Cldn11_Vdac3"
## [1] "Cldn11_Wdfy3"
## [1] "Cnp_Cst3"
## [1] "Cnp_Dnm1l"
## [1] "Cnp_Dnm3"
## [1] "Cnp_Erbb2ip"
## [1] "Cnp_Fam63b"
## [1] "Cnp_Gm15421"
## [1] "Cnp_Gucy1b3"
## [1] "Cnp_Igf2"
## [1] "Cnp_Ildr2"
## [1] "Cnp_Impact"
## [1] "Cnp_Itm2c"
## [1] "Cnp_Luzp2"
## [1] "Cnp_Mlc1"
## [1] "Cnp_Mtor"
## [1] "Cnp_Myo10"
## [1] "Cnp_Nfib"
## [1] "Cnp_Ntng1"
## [1] "Cnp_Plekha1"
## [1] "Cnp_Pmm1"
## [1] "Cnp_Prrc2b"
## [1] "Cnp_Prune2"
## [1] "Cnp_Scd2"
## [1] "Cnp_Slc1a3"
## [1] "Cnp_Smim13"
## [1] "Cnp_Sp8"
## [1] "Cnp_Tiam1"
## [1] "Cnp_Tmem47"
## [1] "Cnp_Tmsb4x"
## [1] "Cnp_Tuba1a"
## [1] "Cnp_Uchl1"
## [1] "Cnp_Utrn"
## [1] "Cnp_Vdac3"
## [1] "Cnp_Wdfy3"
## [1] "Cst3_Dnm1l"
## [1] "Cst3_Dnm3"
## [1] "Cst3_Erbb2ip"
## [1] "Cst3_Fam63b"
## [1] "Cst3_Gm15421"
## [1] "Cst3_Gucy1b3"
## [1] "Cst3_Igf2"
## [1] "Cst3_Ildr2"
## [1] "Cst3_Impact"
## [1] "Cst3_Itm2c"
## [1] "Cst3_Luzp2"
## [1] "Cst3_Mlc1"
## [1] "Cst3_Mtor"
## [1] "Cst3_Myo10"
## [1] "Cst3_Nfib"
## [1] "Cst3_Ntng1"
## [1] "Cst3_Plekha1"
## [1] "Cst3_Pmm1"
## [1] "Cst3_Prrc2b"
## [1] "Cst3_Prune2"
## [1] "Cst3_Scd2"
## [1] "Cst3_Slc1a3"
## [1] "Cst3_Smim13"
## [1] "Cst3_Sp8"
## [1] "Cst3_Tiam1"
## [1] "Cst3_Tmem47"
## [1] "Cst3_Tmsb4x"
## [1] "Cst3_Tuba1a"
## [1] "Cst3_Uchl1"
## [1] "Cst3_Utrn"
## [1] "Cst3_Vdac3"
## [1] "Cst3_Wdfy3"
## [1] "Dnm1l_Dnm3"
## [1] "Dnm1l_Erbb2ip"
## [1] "Dnm1l_Fam63b"
## [1] "Dnm1l_Gm15421"
## [1] "Dnm1l_Gucy1b3"
## [1] "Dnm1l_Igf2"
## [1] "Dnm1l_Ildr2"
## [1] "Dnm1l_Impact"
## [1] "Dnm1l_Itm2c"
## [1] "Dnm1l_Luzp2"
## [1] "Dnm1l_Mlc1"
## [1] "Dnm1l_Mtor"
## [1] "Dnm1l_Myo10"
## [1] "Dnm1l_Nfib"
## [1] "Dnm1l_Ntng1"
## [1] "Dnm1l_Plekha1"
## [1] "Dnm1l_Pmm1"
## [1] "Dnm1l_Prrc2b"
## [1] "Dnm1l_Prune2"
## [1] "Dnm1l_Scd2"
## [1] "Dnm1l_Slc1a3"
## [1] "Dnm1l_Smim13"
## [1] "Dnm1l_Sp8"
## [1] "Dnm1l_Tiam1"
## [1] "Dnm1l_Tmem47"
## [1] "Dnm1l_Tmsb4x"
## [1] "Dnm1l_Tuba1a"
## [1] "Dnm1l_Uchl1"
## [1] "Dnm1l_Utrn"
## [1] "Dnm1l_Vdac3"
## [1] "Dnm1l_Wdfy3"
## [1] "Dnm3_Erbb2ip"
## [1] "Dnm3_Fam63b"
## [1] "Dnm3_Gm15421"
## [1] "Dnm3_Gucy1b3"
## [1] "Dnm3_Igf2"
## [1] "Dnm3_Ildr2"
## [1] "Dnm3_Impact"
## [1] "Dnm3_Itm2c"
## [1] "Dnm3_Luzp2"
## [1] "Dnm3_Mlc1"
## [1] "Dnm3_Mtor"
## [1] "Dnm3_Myo10"
## [1] "Dnm3_Nfib"
## [1] "Dnm3_Ntng1"
## [1] "Dnm3_Plekha1"
## [1] "Dnm3_Pmm1"
## [1] "Dnm3_Prrc2b"
## [1] "Dnm3_Prune2"
## [1] "Dnm3_Scd2"
## [1] "Dnm3_Slc1a3"
## [1] "Dnm3_Smim13"
## [1] "Dnm3_Sp8"
## [1] "Dnm3_Tiam1"
## [1] "Dnm3_Tmem47"
## [1] "Dnm3_Tmsb4x"
## [1] "Dnm3_Tuba1a"
## [1] "Dnm3_Uchl1"
## [1] "Dnm3_Utrn"
## [1] "Dnm3_Vdac3"
## [1] "Dnm3_Wdfy3"
## [1] "Erbb2ip_Fam63b"
## [1] "Erbb2ip_Gm15421"
## [1] "Erbb2ip_Gucy1b3"
## [1] "Erbb2ip_Igf2"
## [1] "Erbb2ip_Ildr2"
## [1] "Erbb2ip_Impact"
## [1] "Erbb2ip_Itm2c"
## [1] "Erbb2ip_Luzp2"
## [1] "Erbb2ip_Mlc1"
## [1] "Erbb2ip_Mtor"
## [1] "Erbb2ip_Myo10"
## [1] "Erbb2ip_Nfib"
## [1] "Erbb2ip_Ntng1"
## [1] "Erbb2ip_Plekha1"
## [1] "Erbb2ip_Pmm1"
## [1] "Erbb2ip_Prrc2b"
## [1] "Erbb2ip_Prune2"
## [1] "Erbb2ip_Scd2"
## [1] "Erbb2ip_Slc1a3"
## [1] "Erbb2ip_Smim13"
## [1] "Erbb2ip_Sp8"
## [1] "Erbb2ip_Tiam1"
## [1] "Erbb2ip_Tmem47"
## [1] "Erbb2ip_Tmsb4x"
## [1] "Erbb2ip_Tuba1a"
## [1] "Erbb2ip_Uchl1"
## [1] "Erbb2ip_Utrn"
## [1] "Erbb2ip_Vdac3"
## [1] "Erbb2ip_Wdfy3"
## [1] "Fam63b_Gm15421"
## [1] "Fam63b_Gucy1b3"
## [1] "Fam63b_Igf2"
## [1] "Fam63b_Ildr2"
## [1] "Fam63b_Impact"
## [1] "Fam63b_Itm2c"
## [1] "Fam63b_Luzp2"
## [1] "Fam63b_Mlc1"
## [1] "Fam63b_Mtor"
## [1] "Fam63b_Myo10"
## [1] "Fam63b_Nfib"
## [1] "Fam63b_Ntng1"
## [1] "Fam63b_Plekha1"
## [1] "Fam63b_Pmm1"
## [1] "Fam63b_Prrc2b"
## [1] "Fam63b_Prune2"
## [1] "Fam63b_Scd2"
## [1] "Fam63b_Slc1a3"
## [1] "Fam63b_Smim13"
## [1] "Fam63b_Sp8"
## [1] "Fam63b_Tiam1"
## [1] "Fam63b_Tmem47"
## [1] "Fam63b_Tmsb4x"
## [1] "Fam63b_Tuba1a"
## [1] "Fam63b_Uchl1"
## [1] "Fam63b_Utrn"
## [1] "Fam63b_Vdac3"
## [1] "Fam63b_Wdfy3"
## [1] "Gm15421_Gucy1b3"
## [1] "Gm15421_Igf2"
## [1] "Gm15421_Ildr2"
## [1] "Gm15421_Impact"
## [1] "Gm15421_Itm2c"
## [1] "Gm15421_Luzp2"
## [1] "Gm15421_Mlc1"
## [1] "Gm15421_Mtor"
## [1] "Gm15421_Myo10"
## [1] "Gm15421_Nfib"
## [1] "Gm15421_Ntng1"
## [1] "Gm15421_Plekha1"
## [1] "Gm15421_Pmm1"
## [1] "Gm15421_Prrc2b"
## [1] "Gm15421_Prune2"
## [1] "Gm15421_Scd2"
## [1] "Gm15421_Slc1a3"
## [1] "Gm15421_Smim13"
## [1] "Gm15421_Sp8"
## [1] "Gm15421_Tiam1"
## [1] "Gm15421_Tmem47"
## [1] "Gm15421_Tmsb4x"
## [1] "Gm15421_Tuba1a"
## [1] "Gm15421_Uchl1"
## [1] "Gm15421_Utrn"
## [1] "Gm15421_Vdac3"
## [1] "Gm15421_Wdfy3"
## [1] "Gucy1b3_Igf2"
## [1] "Gucy1b3_Ildr2"
## [1] "Gucy1b3_Impact"
## [1] "Gucy1b3_Itm2c"
## [1] "Gucy1b3_Luzp2"
## [1] "Gucy1b3_Mlc1"
## [1] "Gucy1b3_Mtor"
## [1] "Gucy1b3_Myo10"
## [1] "Gucy1b3_Nfib"
## [1] "Gucy1b3_Ntng1"
## [1] "Gucy1b3_Plekha1"
## [1] "Gucy1b3_Pmm1"
## [1] "Gucy1b3_Prrc2b"
## [1] "Gucy1b3_Prune2"
## [1] "Gucy1b3_Scd2"
## [1] "Gucy1b3_Slc1a3"
## [1] "Gucy1b3_Smim13"
## [1] "Gucy1b3_Sp8"
## [1] "Gucy1b3_Tiam1"
## [1] "Gucy1b3_Tmem47"
## [1] "Gucy1b3_Tmsb4x"
## [1] "Gucy1b3_Tuba1a"
## [1] "Gucy1b3_Uchl1"
## [1] "Gucy1b3_Utrn"
## [1] "Gucy1b3_Vdac3"
## [1] "Gucy1b3_Wdfy3"
## [1] "Igf2_Ildr2"
## [1] "Igf2_Impact"
## [1] "Igf2_Itm2c"
## [1] "Igf2_Luzp2"
## [1] "Igf2_Mlc1"
## [1] "Igf2_Mtor"
## [1] "Igf2_Myo10"
## [1] "Igf2_Nfib"
## [1] "Igf2_Ntng1"
## [1] "Igf2_Plekha1"
## [1] "Igf2_Pmm1"
## [1] "Igf2_Prrc2b"
## [1] "Igf2_Prune2"
## [1] "Igf2_Scd2"
## [1] "Igf2_Slc1a3"
## [1] "Igf2_Smim13"
## [1] "Igf2_Sp8"
## [1] "Igf2_Tiam1"
## [1] "Igf2_Tmem47"
## [1] "Igf2_Tmsb4x"
## [1] "Igf2_Tuba1a"
## [1] "Igf2_Uchl1"
## [1] "Igf2_Utrn"
## [1] "Igf2_Vdac3"
## [1] "Igf2_Wdfy3"
## [1] "Ildr2_Impact"
## [1] "Ildr2_Itm2c"
## [1] "Ildr2_Luzp2"
## [1] "Ildr2_Mlc1"
## [1] "Ildr2_Mtor"
## [1] "Ildr2_Myo10"
## [1] "Ildr2_Nfib"
## [1] "Ildr2_Ntng1"
## [1] "Ildr2_Plekha1"
## [1] "Ildr2_Pmm1"
## [1] "Ildr2_Prrc2b"
## [1] "Ildr2_Prune2"
## [1] "Ildr2_Scd2"
## [1] "Ildr2_Slc1a3"
## [1] "Ildr2_Smim13"
## [1] "Ildr2_Sp8"
## [1] "Ildr2_Tiam1"
## [1] "Ildr2_Tmem47"
## [1] "Ildr2_Tmsb4x"
## [1] "Ildr2_Tuba1a"
## [1] "Ildr2_Uchl1"
## [1] "Ildr2_Utrn"
## [1] "Ildr2_Vdac3"
## [1] "Ildr2_Wdfy3"
## [1] "Impact_Itm2c"
## [1] "Impact_Luzp2"
## [1] "Impact_Mlc1"
## [1] "Impact_Mtor"
## [1] "Impact_Myo10"
## [1] "Impact_Nfib"
## [1] "Impact_Ntng1"
## [1] "Impact_Plekha1"
## [1] "Impact_Pmm1"
## [1] "Impact_Prrc2b"
## [1] "Impact_Prune2"
## [1] "Impact_Scd2"
## [1] "Impact_Slc1a3"
## [1] "Impact_Smim13"
## [1] "Impact_Sp8"
## [1] "Impact_Tiam1"
## [1] "Impact_Tmem47"
## [1] "Impact_Tmsb4x"
## [1] "Impact_Tuba1a"
## [1] "Impact_Uchl1"
## [1] "Impact_Utrn"
## [1] "Impact_Vdac3"
## [1] "Impact_Wdfy3"
## [1] "Itm2c_Luzp2"
## [1] "Itm2c_Mlc1"
## [1] "Itm2c_Mtor"
## [1] "Itm2c_Myo10"
## [1] "Itm2c_Nfib"
## [1] "Itm2c_Ntng1"
## [1] "Itm2c_Plekha1"
## [1] "Itm2c_Pmm1"
## [1] "Itm2c_Prrc2b"
## [1] "Itm2c_Prune2"
## [1] "Itm2c_Scd2"
## [1] "Itm2c_Slc1a3"
## [1] "Itm2c_Smim13"
## [1] "Itm2c_Sp8"
## [1] "Itm2c_Tiam1"
## [1] "Itm2c_Tmem47"
## [1] "Itm2c_Tmsb4x"
## [1] "Itm2c_Tuba1a"
## [1] "Itm2c_Uchl1"
## [1] "Itm2c_Utrn"
## [1] "Itm2c_Vdac3"
## [1] "Itm2c_Wdfy3"
## [1] "Luzp2_Mlc1"
## [1] "Luzp2_Mtor"
## [1] "Luzp2_Myo10"
## [1] "Luzp2_Nfib"
## [1] "Luzp2_Ntng1"
## [1] "Luzp2_Plekha1"
## [1] "Luzp2_Pmm1"
## [1] "Luzp2_Prrc2b"
## [1] "Luzp2_Prune2"
## [1] "Luzp2_Scd2"
## [1] "Luzp2_Slc1a3"
## [1] "Luzp2_Smim13"
## [1] "Luzp2_Sp8"
## [1] "Luzp2_Tiam1"
## [1] "Luzp2_Tmem47"
## [1] "Luzp2_Tmsb4x"
## [1] "Luzp2_Tuba1a"
## [1] "Luzp2_Uchl1"
## [1] "Luzp2_Utrn"
## [1] "Luzp2_Vdac3"
## [1] "Luzp2_Wdfy3"
## [1] "Mlc1_Mtor"
## [1] "Mlc1_Myo10"
## [1] "Mlc1_Nfib"
## [1] "Mlc1_Ntng1"
## [1] "Mlc1_Plekha1"
## [1] "Mlc1_Pmm1"
## [1] "Mlc1_Prrc2b"
## [1] "Mlc1_Prune2"
## [1] "Mlc1_Scd2"
## [1] "Mlc1_Slc1a3"
## [1] "Mlc1_Smim13"
## [1] "Mlc1_Sp8"
## [1] "Mlc1_Tiam1"
## [1] "Mlc1_Tmem47"
## [1] "Mlc1_Tmsb4x"
## [1] "Mlc1_Tuba1a"
## [1] "Mlc1_Uchl1"
## [1] "Mlc1_Utrn"
## [1] "Mlc1_Vdac3"
## [1] "Mlc1_Wdfy3"
## [1] "Mtor_Myo10"
## [1] "Mtor_Nfib"
## [1] "Mtor_Ntng1"
## [1] "Mtor_Plekha1"
## [1] "Mtor_Pmm1"
## [1] "Mtor_Prrc2b"
## [1] "Mtor_Prune2"
## [1] "Mtor_Scd2"
## [1] "Mtor_Slc1a3"
## [1] "Mtor_Smim13"
## [1] "Mtor_Sp8"
## [1] "Mtor_Tiam1"
## [1] "Mtor_Tmem47"
## [1] "Mtor_Tmsb4x"
## [1] "Mtor_Tuba1a"
## [1] "Mtor_Uchl1"
## [1] "Mtor_Utrn"
## [1] "Mtor_Vdac3"
## [1] "Mtor_Wdfy3"
## [1] "Myo10_Nfib"
## [1] "Myo10_Ntng1"
## [1] "Myo10_Plekha1"
## [1] "Myo10_Pmm1"
## [1] "Myo10_Prrc2b"
## [1] "Myo10_Prune2"
## [1] "Myo10_Scd2"
## [1] "Myo10_Slc1a3"
## [1] "Myo10_Smim13"
## [1] "Myo10_Sp8"
## [1] "Myo10_Tiam1"
## [1] "Myo10_Tmem47"
## [1] "Myo10_Tmsb4x"
## [1] "Myo10_Tuba1a"
## [1] "Myo10_Uchl1"
## [1] "Myo10_Utrn"
## [1] "Myo10_Vdac3"
## [1] "Myo10_Wdfy3"
## [1] "Nfib_Ntng1"
## [1] "Nfib_Plekha1"
## [1] "Nfib_Pmm1"
## [1] "Nfib_Prrc2b"
## [1] "Nfib_Prune2"
## [1] "Nfib_Scd2"
## [1] "Nfib_Slc1a3"
## [1] "Nfib_Smim13"
## [1] "Nfib_Sp8"
## [1] "Nfib_Tiam1"
## [1] "Nfib_Tmem47"
## [1] "Nfib_Tmsb4x"
## [1] "Nfib_Tuba1a"
## [1] "Nfib_Uchl1"
## [1] "Nfib_Utrn"
## [1] "Nfib_Vdac3"
## [1] "Nfib_Wdfy3"
## [1] "Ntng1_Plekha1"
## [1] "Ntng1_Pmm1"
## [1] "Ntng1_Prrc2b"
## [1] "Ntng1_Prune2"
## [1] "Ntng1_Scd2"
## [1] "Ntng1_Slc1a3"
## [1] "Ntng1_Smim13"
## [1] "Ntng1_Sp8"
## [1] "Ntng1_Tiam1"
## [1] "Ntng1_Tmem47"
## [1] "Ntng1_Tmsb4x"
## [1] "Ntng1_Tuba1a"
## [1] "Ntng1_Uchl1"
## [1] "Ntng1_Utrn"
## [1] "Ntng1_Vdac3"
## [1] "Ntng1_Wdfy3"
## [1] "Plekha1_Pmm1"
## [1] "Plekha1_Prrc2b"
## [1] "Plekha1_Prune2"
## [1] "Plekha1_Scd2"
## [1] "Plekha1_Slc1a3"
## [1] "Plekha1_Smim13"
## [1] "Plekha1_Sp8"
## [1] "Plekha1_Tiam1"
## [1] "Plekha1_Tmem47"
## [1] "Plekha1_Tmsb4x"
## [1] "Plekha1_Tuba1a"
## [1] "Plekha1_Uchl1"
## [1] "Plekha1_Utrn"
## [1] "Plekha1_Vdac3"
## [1] "Plekha1_Wdfy3"
## [1] "Pmm1_Prrc2b"
## [1] "Pmm1_Prune2"
## [1] "Pmm1_Scd2"
## [1] "Pmm1_Slc1a3"
## [1] "Pmm1_Smim13"
## [1] "Pmm1_Sp8"
## [1] "Pmm1_Tiam1"
## [1] "Pmm1_Tmem47"
## [1] "Pmm1_Tmsb4x"
## [1] "Pmm1_Tuba1a"
## [1] "Pmm1_Uchl1"
## [1] "Pmm1_Utrn"
## [1] "Pmm1_Vdac3"
## [1] "Pmm1_Wdfy3"
## [1] "Prrc2b_Prune2"
## [1] "Prrc2b_Scd2"
## [1] "Prrc2b_Slc1a3"
## [1] "Prrc2b_Smim13"
## [1] "Prrc2b_Sp8"
## [1] "Prrc2b_Tiam1"
## [1] "Prrc2b_Tmem47"
## [1] "Prrc2b_Tmsb4x"
## [1] "Prrc2b_Tuba1a"
## [1] "Prrc2b_Uchl1"
## [1] "Prrc2b_Utrn"
## [1] "Prrc2b_Vdac3"
## [1] "Prrc2b_Wdfy3"
## [1] "Prune2_Scd2"
## [1] "Prune2_Slc1a3"
## [1] "Prune2_Smim13"
## [1] "Prune2_Sp8"
## [1] "Prune2_Tiam1"
## [1] "Prune2_Tmem47"
## [1] "Prune2_Tmsb4x"
## [1] "Prune2_Tuba1a"
## [1] "Prune2_Uchl1"
## [1] "Prune2_Utrn"
## [1] "Prune2_Vdac3"
## [1] "Prune2_Wdfy3"
## [1] "Scd2_Slc1a3"
## [1] "Scd2_Smim13"
## [1] "Scd2_Sp8"
## [1] "Scd2_Tiam1"
## [1] "Scd2_Tmem47"
## [1] "Scd2_Tmsb4x"
## [1] "Scd2_Tuba1a"
## [1] "Scd2_Uchl1"
## [1] "Scd2_Utrn"
## [1] "Scd2_Vdac3"
## [1] "Scd2_Wdfy3"
## [1] "Slc1a3_Smim13"
## [1] "Slc1a3_Sp8"
## [1] "Slc1a3_Tiam1"
## [1] "Slc1a3_Tmem47"
## [1] "Slc1a3_Tmsb4x"
## [1] "Slc1a3_Tuba1a"
## [1] "Slc1a3_Uchl1"
## [1] "Slc1a3_Utrn"
## [1] "Slc1a3_Vdac3"
## [1] "Slc1a3_Wdfy3"
## [1] "Smim13_Sp8"
## [1] "Smim13_Tiam1"
## [1] "Smim13_Tmem47"
## [1] "Smim13_Tmsb4x"
## [1] "Smim13_Tuba1a"
## [1] "Smim13_Uchl1"
## [1] "Smim13_Utrn"
## [1] "Smim13_Vdac3"
## [1] "Smim13_Wdfy3"
## [1] "Sp8_Tiam1"
## [1] "Sp8_Tmem47"
## [1] "Sp8_Tmsb4x"
## [1] "Sp8_Tuba1a"
## [1] "Sp8_Uchl1"
## [1] "Sp8_Utrn"
## [1] "Sp8_Vdac3"
## [1] "Sp8_Wdfy3"
## [1] "Tiam1_Tmem47"
## [1] "Tiam1_Tmsb4x"
## [1] "Tiam1_Tuba1a"
## [1] "Tiam1_Uchl1"
## [1] "Tiam1_Utrn"
## [1] "Tiam1_Vdac3"
## [1] "Tiam1_Wdfy3"
## [1] "Tmem47_Tmsb4x"
## [1] "Tmem47_Tuba1a"
## [1] "Tmem47_Uchl1"
## [1] "Tmem47_Utrn"
## [1] "Tmem47_Vdac3"
## [1] "Tmem47_Wdfy3"
## [1] "Tmsb4x_Tuba1a"
## [1] "Tmsb4x_Uchl1"
## [1] "Tmsb4x_Utrn"
## [1] "Tmsb4x_Vdac3"
## [1] "Tmsb4x_Wdfy3"
## [1] "Tuba1a_Uchl1"
## [1] "Tuba1a_Utrn"
## [1] "Tuba1a_Vdac3"
## [1] "Tuba1a_Wdfy3"
## [1] "Uchl1_Utrn"
## [1] "Uchl1_Vdac3"
## [1] "Uchl1_Wdfy3"
## [1] "Utrn_Vdac3"
## [1] "Utrn_Wdfy3"
## [1] "Vdac3_Wdfy3"p_all$gene1 = unlist(lapply(strsplit(as.character(p_all$genepair), "_"), "[", 1))
p_all$gene2 = unlist(lapply(strsplit(as.character(p_all$genepair), "_"), "[", 2))
# differentially expressed genes to remove
p_all$spatiallyDE = ifelse(as.character(p_all$gene1) %in% nonDEgenes & as.character(p_all$gene2) %in% nonDEgenes,"No", "DE")
dim(subset(p_all, spatiallyDE == "No"))## [1] 903 11nonDEfdr = p_all$pval
nonDEfdr[p_all$spatiallyDE == "DE"] <- NA
nonDEfdr = p.adjust(nonDEfdr, method = "BH")
nonDEfdr[is.na(nonDEfdr)] <- 1
p_all$nonDEfdr = nonDEfdr
getDF = function(gene1, gene2 = NULL) {
if (length(gene1) > 1) {
gene2 = gene1[2]
gene1 = gene1[1]
}
gpair = paste0(gene1,"_",gene2)
if (!gpair %in% rownames(wcors_all)) {
gpair = paste0(gene2,"_",gene1)
}
wcor = wcors_all[gpair,]
df_res = data.frame(x = coords[,"x"],
y = coords[,"y"],
g1 = expr[gene1,],
g2 = expr[gene2,],
wcor = wcor,
W_min = W[which.min(wcor),],
W_max = W[which.max(wcor),])
return(df_res)
}
basicplotFunction = function(gene1, gene2 = NULL) {
require(ggforce)
require(patchwork)
require(ggpubr)
if (length(gene1) > 1) {
gene2 = gene1[2]
gene1 = gene1[1]
}
df_res = getDF(gene1, gene2)
t = theme(legend.key.width = unit(0.5, "inches")) +
theme(plot.title = element_text(size = 20)) +
theme(axis.title = element_text(size = 15))
g_gene1 = ggplot(df_res, aes(x = -x, y = y)) +
geom_point(aes(colour = g1), size = 5) +
theme_minimal() +
theme(panel.grid = element_blank()) +
theme(axis.text = element_blank()) +
xlab("") +
ylab("") +
ggtitle(gene1) +
labs(colour = "") +
theme(legend.position = "bottom") +
theme(plot.title = element_text(hjust = 0.5, face = "italic")) +
scale_color_viridis_c(breaks = c(0,max(df_res$g1)),
limits = c(0,max(df_res$g1)),
labels = c("Low","High")) +
t +
coord_fixed() +
guides(colour = guide_colourbar(title.position = "top",
title.hjust = 0.5)) +
theme(legend.title=element_text(size=15)) +
labs(colour = "Expression") +
NULL
g_gene2 = ggplot(df_res, aes(x = -x, y = y)) +
geom_point(aes(colour = g2), size = 5) +
theme_minimal() +
theme(panel.grid = element_blank()) +
theme(axis.text = element_blank()) +
xlab("") +
ylab("") +
ggtitle(gene2) +
theme(plot.title = element_text(hjust = 0.5, face = "italic")) +
labs(colour = "") +
theme(legend.position = "bottom") +
scale_color_viridis_c(breaks = c(0,max(df_res$g1)),
limits = c(0,max(df_res$g1)),
labels = c("Low","High")) +
t +
coord_fixed() +
theme(legend.position = "none") +
NULL
g2 = ggplot(df_res, aes(x = -x, y = y, fill = wcor)) +
geom_voronoi_tile(max.radius = 1) +
theme_minimal() +
theme(panel.grid = element_blank()) +
theme(axis.text = element_blank()) +
theme(plot.title = element_text(hjust = 0.5)) +
theme(legend.position = "bottom") +
labs(colour = "",fill = "") +
labs(colour = "Local correlation",fill = "Local correlation") +
ylab("") +
xlab("") +
ggtitle("Correlation of both genes") +
scale_alpha_continuous(range = c(0,0.5)) +
scale_fill_gradient2(low = "blue", mid = "white", high = "red", limits = c(-1,1)) +
t +
coord_fixed() +
guides(fill = guide_colourbar(title.position = "top",
title.hjust = 0.5)) +
theme(legend.title=element_text(size=15)) +
NULL
g_gene1_leg = as_ggplot(get_legend(g_gene1))
g2_leg = as_ggplot(get_legend(g2))
scater::multiplot(g_gene1 + theme(legend.position = "none") +
theme(plot.margin = margin(10,0,-10,0)),
g_gene2 +
theme(plot.margin = margin(10,0,-10,0)),
g2 + theme(legend.position = "none") +
theme(plot.margin = margin(10,0,-10,0)),
g_gene1_leg,
g2_leg,
layout = matrix(
c(1,1,2,2,3,3,
1,1,2,2,3,3,
1,1,2,2,3,3,
6,4,4,6,5,5), ncol = 6, byrow = TRUE))
}
plotFunction = function(gene1, gene2 = NULL) {
require(ggforce)
require(patchwork)
if (length(gene1) > 1) {
gene2 = gene1[2]
gene1 = gene1[1]
}
df_res = getDF(gene1, gene2)
g_W_min = ggplot(df_res, aes(x = g1, y = g2)) +
geom_point(aes(alpha = W_min, size = W_min), colour = "purple") +
theme_minimal() +
xlab(gene1) +
ylab(gene2) +
ggtitle("Min") +
NULL
g_W_max = ggplot(df_res, aes(x = g1, y = g2)) +
geom_point(aes(alpha = W_max, size = W_max), colour = "orange") +
theme_minimal() +
xlab(gene1) +
ylab(gene2) +
ggtitle("Max") +
NULL
g_xy = ggplot(df_res, aes(x = x, y = y)) +
geom_point(size = 0.1) +
geom_density_2d(data = subset(df_res, W_max != 0), colour = "orange") +
geom_density_2d(data = subset(df_res, W_min != 0), colour = "purple") +
theme_minimal() +
xlab("x coordinate") +
ylab("y coordinate") +
ggtitle("Positions") +
NULL
g_gene1 = ggplot(df_res, aes(x = x, y = y)) +
geom_point(aes(colour = g1), size = 5) +
theme_minimal() +
ggtitle(gene1) +
scale_color_gradient2(low = "black", mid = "yellow", high = "red", midpoint = 2) +
NULL
g_gene2 = ggplot(df_res, aes(x = x, y = y)) +
geom_point(aes(colour = g2), size = 5) +
theme_minimal() +
ggtitle(gene2) +
scale_color_gradient2(low = "black", mid = "yellow", high = "red", midpoint = 2) +
NULL
g2 = ggplot(df_res, aes(x = x, y = y, fill = wcor)) +
geom_voronoi_tile(max.radius = 1) +
geom_point(size = 1, colour = "black") +
theme_minimal() +
scale_alpha_continuous(range = c(0,0.5)) +
scale_fill_gradient2(low = "blue", mid = "white", high = "red", limits = c(-1,1)) +
NULL
return(g_gene1 + g_gene2 + g2 +
g_W_min + g_W_max + g_xy + plot_layout(ncol = 3, nrow = 2, byrow = TRUE))
}
FDR_level = 0.2
wcorsSig = wcors_all[p_all$nonDEfdr < FDR_level,]
pairsSig = pairs[p_all$nonDEfdr < FDR_level,]
dim(wcorsSig)## [1] 167 262# basic plot functions of sig pairs
apply(pairsSig,1, function(p) {
#print(p)
if (!file.exists("output/basicplots")) {
system("mkdir output/basicplots")
}
pdf(paste0("output/basicplots/", p[1], "_", p[2], ".pdf"),
height = 4.5, width = 12,onefile=FALSE)
basicplotFunction(p)
dev.off()
})## Abat_Arrb1 Abat_Cst3 Abat_Mlc1 Abat_Myo10
## 2 2 2 2
## Abat_Slc1a3 Abat_Tiam1 Actb_Gucy1b3 Actb_Itm2c
## 2 2 2 2
## Actb_Myo10 Actb_Smim13 Actb_Sp8 Actb_Tiam1
## 2 2 2 2
## Actb_Vdac3 Arrb1_Cnp Arrb1_Cst3 Arrb1_Dnm3
## 2 2 2 2
## Arrb1_Mtor Arrb1_Prune2 Arrb1_Smim13 Arrb1_Sp8
## 2 2 2 2
## Arrb1_Tmem47 Arrb1_Uchl1 Atp6v1c1_Calm1 Atp6v1c1_Cst3
## 2 2 2 2
## Atp6v1c1_Luzp2 Atp6v1c1_Mlc1 Atp6v1c1_Myo10 Atp6v1c1_Plekha1
## 2 2 2 2
## Atp6v1c1_Sp8 Atp6v1c1_Tiam1 Atp6v1c1_Tmsb4x Atrnl1_Ccng1
## 2 2 2 2
## Atrnl1_Gm15421 Atrnl1_Myo10 Bai1_Ccng1 Bai1_Cst3
## 2 2 2 2
## Bai1_Gucy1b3 Bai1_Slc1a3 Bai1_Tiam1 Calm1_Cst3
## 2 2 2 2
## Calm1_Dnm1l Calm1_Gucy1b3 Calm1_Plekha1 Calm1_Smim13
## 2 2 2 2
## Calm1_Sp8 Calm1_Tiam1 Calm1_Vdac3 Calm1_Wdfy3
## 2 2 2 2
## Ccng1_Cldn11 Ccng1_Erbb2ip Ccng1_Scd2 Ccng1_Smim13
## 2 2 2 2
## Cldn11_Cnp Cldn11_Cst3 Cldn11_Gucy1b3 Cldn11_Ildr2
## 2 2 2 2
## Cldn11_Itm2c Cldn11_Scd2 Cldn11_Tuba1a Cldn11_Vdac3
## 2 2 2 2
## Cnp_Itm2c Cnp_Prune2 Cnp_Tmsb4x Cst3_Gucy1b3
## 2 2 2 2
## Cst3_Impact Cst3_Itm2c Cst3_Luzp2 Cst3_Mtor
## 2 2 2 2
## Cst3_Myo10 Cst3_Prrc2b Cst3_Prune2 Cst3_Smim13
## 2 2 2 2
## Cst3_Sp8 Cst3_Tuba1a Cst3_Uchl1 Cst3_Wdfy3
## 2 2 2 2
## Dnm1l_Dnm3 Dnm1l_Fam63b Dnm1l_Plekha1 Dnm1l_Sp8
## 2 2 2 2
## Dnm1l_Vdac3 Dnm3_Fam63b Dnm3_Tiam1 Gm15421_Ildr2
## 2 2 2 2
## Gm15421_Itm2c Gm15421_Tmsb4x Gucy1b3_Ildr2 Gucy1b3_Mlc1
## 2 2 2 2
## Gucy1b3_Myo10 Gucy1b3_Plekha1 Gucy1b3_Smim13 Gucy1b3_Tiam1
## 2 2 2 2
## Gucy1b3_Tmem47 Gucy1b3_Tmsb4x Gucy1b3_Tuba1a Gucy1b3_Uchl1
## 2 2 2 2
## Igf2_Mtor Igf2_Pmm1 Ildr2_Itm2c Ildr2_Mlc1
## 2 2 2 2
## Ildr2_Plekha1 Ildr2_Tiam1 Ildr2_Tuba1a Impact_Mlc1
## 2 2 2 2
## Impact_Myo10 Impact_Ntng1 Impact_Plekha1 Impact_Tiam1
## 2 2 2 2
## Impact_Tmem47 Itm2c_Myo10 Itm2c_Pmm1 Itm2c_Prrc2b
## 2 2 2 2
## Itm2c_Smim13 Itm2c_Sp8 Itm2c_Tiam1 Itm2c_Tuba1a
## 2 2 2 2
## Itm2c_Uchl1 Itm2c_Vdac3 Luzp2_Uchl1 Mlc1_Mtor
## 2 2 2 2
## Mlc1_Myo10 Mlc1_Prune2 Mlc1_Slc1a3 Mlc1_Uchl1
## 2 2 2 2
## Mtor_Myo10 Mtor_Slc1a3 Mtor_Tmem47 Mtor_Vdac3
## 2 2 2 2
## Mtor_Wdfy3 Myo10_Prune2 Myo10_Scd2 Myo10_Slc1a3
## 2 2 2 2
## Myo10_Sp8 Myo10_Tiam1 Myo10_Uchl1 Ntng1_Tiam1
## 2 2 2 2
## Ntng1_Utrn Plekha1_Tiam1 Plekha1_Tmsb4x Plekha1_Vdac3
## 2 2 2 2
## Prrc2b_Sp8 Prrc2b_Tiam1 Prrc2b_Vdac3 Prune2_Tiam1
## 2 2 2 2
## Prune2_Tuba1a Prune2_Wdfy3 Scd2_Smim13 Scd2_Sp8
## 2 2 2 2
## Smim13_Sp8 Smim13_Tmem47 Smim13_Tmsb4x Smim13_Tuba1a
## 2 2 2 2
## Smim13_Vdac3 Sp8_Tmsb4x Sp8_Tuba1a Sp8_Uchl1
## 2 2 2 2
## Sp8_Vdac3 Tiam1_Tmsb4x Tiam1_Tuba1a Tiam1_Vdac3
## 2 2 2 2
## Tiam1_Wdfy3 Tmsb4x_Tuba1a Tmsb4x_Vdac3 Tuba1a_Uchl1
## 2 2 2 2
## Tuba1a_Vdac3 Uchl1_Vdac3 Vdac3_Wdfy3
## 2 2 2Interrogate significant gene pairs
cellsCut = cutree(hclust(cordist(t(wcorsSig))), 20)
table(cellsCut)## cellsCut
## 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## 15 16 19 10 7 12 18 4 6 27 6 9 36 10 12 8 12 8 7 20sort(table(cellsCut))## cellsCut
## 8 9 11 5 19 16 18 12 4 14 6 15 17 1 2 7 3 20 10 13
## 4 6 6 7 7 8 8 9 10 10 12 12 12 15 16 18 19 20 27 36df_res = getDF(pairs[1,])
df_res$cellsCut <- factor(cellsCut)
ggplot(df_res, aes(x = x, y = y, fill = cellsCut, colour = cellsCut)) +
geom_point(size = 7, shape = 21, stroke = 1.5, colour = "black") +
theme_minimal() +
scale_alpha_continuous(range = c(0,0.5)) +
NULL
ggsave(file = "output/cellsCluster_spatial.pdf", height = 8, width = 10)
hc = hclust(dist(wcorsSig, method = "maximum"), method = "ward.D2")
genepairsClustDynamic = cutreeDynamic(
hc,
minClusterSize = 10,
method = "tree",
deepSplit = TRUE,
useMedoids = FALSE
)
kk = length(unique(genepairsClustDynamic))-1
kk## [1] 8genepairsClust = cutree(hc, k = kk)
plot(hc)
table(genepairsClust)## genepairsClust
## 1 2 3 4 5 6 7 8
## 27 31 35 26 7 13 20 8sort(table(genepairsClust))## genepairsClust
## 5 8 6 7 4 1 2 3
## 7 8 13 20 26 27 31 35p_sig = cbind(p_all[names(genepairsClust),], cluster = genepairsClust)
saveRDS(p_sig, file = "output/p_sig.Rds")
write.table(as.matrix(sort_df(p_sig, c("cluster","genepair"))),
file = "output/sig_genepairs.tsv", row.names = FALSE,
col.names = TRUE, quote = FALSE, sep = "\t")
write.table(as.matrix(genepairsClust), file = "output/genepairsClust.tsv", row.names = TRUE,
col.names = FALSE, quote = FALSE, sep = "\t")
genepairs_split = lapply(split(names(genepairsClust), genepairsClust), function(x) t(do.call(cbind, strsplit(x, "_"))))
genepairs_split_genes = lapply(genepairs_split, function(x) sort(unique(c(x))))
sapply(names(genepairs_split_genes), function(i){
write(genepairs_split_genes[[i]], file = paste0("output/cluster_", i,".txt"))
})## $`1`
## NULL
##
## $`2`
## NULL
##
## $`3`
## NULL
##
## $`4`
## NULL
##
## $`5`
## NULL
##
## $`6`
## NULL
##
## $`7`
## NULL
##
## $`8`
## NULLgeneClustMembers = sapply(unique(genepairsClust), function(x)
unique(c(pairsSig[genepairsClust == x,])), simplify = FALSE)
names(geneClustMembers) <- paste0("cluster_", unique(genepairsClust))
jacDist_pairs = expand.grid(names(geneClustMembers),names(geneClustMembers))
jacDist_vals = apply(jacDist_pairs,1,function(x){
if (x[1] == x[2]) return(NA)
set1 = geneClustMembers[[x[1]]]
set2 = geneClustMembers[[x[2]]]
return(length(intersect(set1,set2))/length(union(set1,set2)))
})
jacDist = as.matrix(reshape::cast(cbind(jacDist_pairs, jacDist_vals), formula = Var2 ~ Var1, value = "jacDist_vals"))
pdf("output/jacDist_clusters.pdf", height = 8, width = 8)
heatmap.2(jacDist, trace = "n", main = "Jaccard distance of genes within clusters",
density.info = "none",
key.title = "",
key.xlab = "Jaccard distance",
symm = TRUE,
revC = TRUE)
dev.off()## quartz_off_screen
## 2meanwcorsSig = apply(wcorsSig, 2, function(x) {
tapply(x, genepairsClust, mean)
})
rownames(meanwcorsSig) <- paste0("cluster_", 1:length(unique(genepairsClust)))
pdf("output/meanGenes_heatmap.pdf", height = 12, width = 24)
heatmap.2(meanwcorsSig, trace = "n", col = colorRampPalette(c("blue","white","red")),
key.title = "",
key.xlab = "Mean weighted correlation",
main = "Mean weighted correlation of clustered genepairs")
dev.off()## quartz_off_screen
## 2df_res2 <- getDF(pairs[1,])
df_res2 <- cbind(df_res2, t(meanwcorsSig))
gList_cells <- sapply(rownames(meanwcorsSig), function(name) {
ggplot(df_res2, aes(x = -x, y = y, fill = get(name))) +
geom_voronoi_tile(max.radius = 1) +
geom_point(size = 0.5, colour = "black") +
theme_minimal() +
scale_alpha_continuous(range = c(0,0.5)) +
scale_fill_gradient2(low = "blue", mid = "white", high = "red", limits = c(-1,1)) +
ggtitle("") +
theme(legend.position = "none") +
theme(panel.grid = element_blank()) +
theme(axis.ticks = element_blank()) +
theme(axis.text = element_blank()) +
xlab("") + ylab("") +
theme(plot.title = element_text(hjust = 0.5)) +
coord_fixed() +
NULL
}, simplify = FALSE)
gAll = patchwork::wrap_plots(gList_cells, ncol = length(gList_cells)/5, nrow = 5)
gAll
ggsave(gAll, file = "output/genepairsClust_wcors.pdf", height = 5, width = 44)
hc_mean_cells = hclust(dist(t(wcorsSig), method = "maximum"), method = "ward.D2")
hc_mean_cells_groups = cutreeDynamic(
hc_mean_cells,
minClusterSize = 10,
method = "tree",
deepSplit = FALSE,
useMedoids = FALSE
)
kk_cells = length(unique(hc_mean_cells_groups))-1
kk_cells## [1] 5hc_mean_cells_groups = cutree(hc_mean_cells, kk_cells)
plot(hc_mean_cells)
plot(hc_mean_cells, labels = hc_mean_cells_groups)
hc_mean_cells_fac = factor(hc_mean_cells_groups, levels = unique(hc_mean_cells_groups[hc_mean_cells$order]))
df_hc_mean_cells = data.frame(
x = coords[,1],
y = coords[,2],
hc_mean_cells = hc_mean_cells_fac
)
s = 1
g_cells = ggplot(df_hc_mean_cells, aes(x = -x, y = y)) +
geom_point(data = df_hc_mean_cells[,1:2], alpha = 0.2, stroke = 0, size = s, pch = 16) +
geom_point(stroke = 0, size = s, pch = 16) +
facet_grid(hc_mean_cells~.) +
theme_minimal() +
theme(panel.grid = element_blank(),
axis.text = element_blank()) +
xlab("") +
ylab("") +
coord_fixed() +
NULL
g_cells
ggsave(g_cells, file = "output/split_heatmap_cells.pdf",height = 7, width = 1.5)
hc_mean_genepairs = hc
hc_mean_genepairs_groups = genepairsClust
plot(hc_mean_genepairs)
plot(hc_mean_genepairs, labels = hc_mean_genepairs_groups)
hc_mean_genepairs_fac = factor(hc_mean_genepairs_groups, levels = unique(hc_mean_genepairs_groups[hc_mean_genepairs$order]))
split(names(hc_mean_genepairs_fac), hc_mean_genepairs_fac)## $`8`
## [1] "Bai1_Ccng1" "Ccng1_Cldn11" "Ccng1_Erbb2ip" "Ccng1_Scd2"
## [5] "Ccng1_Smim13" "Dnm3_Fam63b" "Igf2_Mtor" "Impact_Ntng1"
##
## $`2`
## [1] "Abat_Cst3" "Abat_Mlc1" "Abat_Slc1a3" "Arrb1_Tmem47"
## [5] "Atp6v1c1_Cst3" "Atp6v1c1_Luzp2" "Atp6v1c1_Mlc1" "Bai1_Cst3"
## [9] "Bai1_Gucy1b3" "Bai1_Slc1a3" "Cldn11_Gucy1b3" "Cst3_Gucy1b3"
## [13] "Cst3_Impact" "Cst3_Prune2" "Gucy1b3_Mlc1" "Gucy1b3_Tmem47"
## [17] "Gucy1b3_Uchl1" "Ildr2_Mlc1" "Impact_Mlc1" "Impact_Tmem47"
## [21] "Itm2c_Uchl1" "Mlc1_Prune2" "Mlc1_Uchl1" "Mtor_Myo10"
## [25] "Mtor_Slc1a3" "Mtor_Tmem47" "Myo10_Prune2" "Myo10_Slc1a3"
## [29] "Prune2_Tuba1a" "Smim13_Tmem47" "Uchl1_Vdac3"
##
## $`1`
## [1] "Abat_Arrb1" "Abat_Myo10" "Actb_Myo10" "Arrb1_Cnp"
## [5] "Arrb1_Dnm3" "Arrb1_Mtor" "Arrb1_Prune2" "Arrb1_Smim13"
## [9] "Arrb1_Sp8" "Arrb1_Uchl1" "Atp6v1c1_Myo10" "Atrnl1_Myo10"
## [13] "Cst3_Mtor" "Cst3_Myo10" "Cst3_Sp8" "Cst3_Uchl1"
## [17] "Dnm1l_Fam63b" "Gucy1b3_Myo10" "Impact_Myo10" "Itm2c_Myo10"
## [21] "Luzp2_Uchl1" "Mlc1_Mtor" "Mlc1_Myo10" "Myo10_Scd2"
## [25] "Myo10_Sp8" "Myo10_Uchl1" "Sp8_Uchl1"
##
## $`3`
## [1] "Abat_Tiam1" "Actb_Tiam1" "Atp6v1c1_Plekha1"
## [4] "Atp6v1c1_Tiam1" "Atrnl1_Ccng1" "Atrnl1_Gm15421"
## [7] "Bai1_Tiam1" "Calm1_Tiam1" "Cldn11_Ildr2"
## [10] "Cldn11_Tuba1a" "Cldn11_Vdac3" "Cnp_Prune2"
## [13] "Dnm1l_Dnm3" "Dnm3_Tiam1" "Gm15421_Ildr2"
## [16] "Gucy1b3_Ildr2" "Gucy1b3_Plekha1" "Gucy1b3_Smim13"
## [19] "Igf2_Pmm1" "Ildr2_Itm2c" "Ildr2_Plekha1"
## [22] "Ildr2_Tiam1" "Ildr2_Tuba1a" "Impact_Plekha1"
## [25] "Impact_Tiam1" "Itm2c_Pmm1" "Myo10_Tiam1"
## [28] "Ntng1_Tiam1" "Plekha1_Tiam1" "Prrc2b_Tiam1"
## [31] "Prune2_Tiam1" "Tiam1_Tmsb4x" "Tiam1_Tuba1a"
## [34] "Tiam1_Vdac3" "Tiam1_Wdfy3"
##
## $`5`
## [1] "Actb_Smim13" "Calm1_Smim13" "Cst3_Smim13" "Itm2c_Smim13"
## [5] "Scd2_Smim13" "Smim13_Tmsb4x" "Smim13_Tuba1a"
##
## $`6`
## [1] "Actb_Sp8" "Atp6v1c1_Sp8" "Calm1_Dnm1l" "Calm1_Sp8"
## [5] "Cldn11_Cnp" "Dnm1l_Sp8" "Itm2c_Sp8" "Prrc2b_Sp8"
## [9] "Scd2_Sp8" "Sp8_Tmsb4x" "Sp8_Tuba1a" "Sp8_Vdac3"
## [13] "Tmsb4x_Tuba1a"
##
## $`4`
## [1] "Actb_Gucy1b3" "Actb_Itm2c" "Actb_Vdac3"
## [4] "Atp6v1c1_Calm1" "Atp6v1c1_Tmsb4x" "Calm1_Gucy1b3"
## [7] "Calm1_Plekha1" "Calm1_Vdac3" "Calm1_Wdfy3"
## [10] "Cnp_Itm2c" "Cnp_Tmsb4x" "Dnm1l_Plekha1"
## [13] "Dnm1l_Vdac3" "Gucy1b3_Tiam1" "Gucy1b3_Tmsb4x"
## [16] "Gucy1b3_Tuba1a" "Itm2c_Prrc2b" "Itm2c_Tiam1"
## [19] "Itm2c_Tuba1a" "Itm2c_Vdac3" "Mtor_Wdfy3"
## [22] "Plekha1_Tmsb4x" "Prrc2b_Vdac3" "Tmsb4x_Vdac3"
## [25] "Tuba1a_Vdac3" "Vdac3_Wdfy3"
##
## $`7`
## [1] "Arrb1_Cst3" "Calm1_Cst3" "Cldn11_Cst3" "Cldn11_Itm2c"
## [5] "Cldn11_Scd2" "Cst3_Itm2c" "Cst3_Luzp2" "Cst3_Prrc2b"
## [9] "Cst3_Tuba1a" "Cst3_Wdfy3" "Gm15421_Itm2c" "Gm15421_Tmsb4x"
## [13] "Mlc1_Slc1a3" "Mtor_Vdac3" "Ntng1_Utrn" "Plekha1_Vdac3"
## [17] "Prune2_Wdfy3" "Smim13_Sp8" "Smim13_Vdac3" "Tuba1a_Uchl1"write.table(sort_df(data.frame(grouping = hc_mean_genepairs_fac, cluster = names(hc_mean_genepairs_fac)), "grouping"), file = "output/hc_mean_genepairs_fac_split.txt", col.names = TRUE, row.names = FALSE, quote = FALSE, sep = "\t")
hc_mean_meanwcorsSig = apply(wcorsSig, 2, function(x)
tapply(x, hc_mean_genepairs_fac, mean)
)
df_hc_mean_genepairs = data.frame(
x = rep(coords[,1],times = nrow(hc_mean_meanwcorsSig)),
y = rep(coords[,2],times = nrow(hc_mean_meanwcorsSig)),
hc_mean_genepairs = factor(rep(levels(hc_mean_genepairs_fac), each = ncol(meanwcorsSig)),
levels = levels(hc_mean_genepairs_fac)),
hc_mean_genepairs_wc = c(t(hc_mean_meanwcorsSig))
)
g_mean = ggplot(df_hc_mean_genepairs, aes(x = -x, y = y, colour = hc_mean_genepairs_wc)) +
geom_point(size = 0.7) +
facet_grid(~hc_mean_genepairs) +
theme_minimal() +
theme(panel.grid = element_blank(),
axis.text = element_blank()) +
scale_colour_gradient2(low = "blue", mid = "white", high = "red", limits = c(-1,1)) +
theme(legend.position = "none") +
xlab("") +
ylab("") +
coord_fixed() +
NULL
g_mean
cowplot::ggsave2(g_mean, file = "output/split_heatmap_genepairs.pdf", height = 1.3, width = 9)
pdf("output/split_heatmap.pdf",height = 10, width = 15)
tmat = t(wcorsSig)
colnames(tmat) <- gsub("cluster_","", colnames(tmat))
h = ComplexHeatmap::Heatmap(tmat,
cluster_columns = hc_mean_genepairs,
cluster_rows = hc_mean_cells,
row_dend_reorder = FALSE,
column_dend_reorder = FALSE,
row_split = kk_cells,
column_split = kk,
show_heatmap_legend = FALSE,
show_column_names = FALSE
)
print(h)
dev.off()## quartz_off_screen
## 2grob = grid.grabExpr(draw(h))
tmatmean = t(apply(tmat, 1, function(x) tapply(x, hc_mean_genepairs_fac, mean)))
hh = ComplexHeatmap::Heatmap(tmatmean, cluster_columns = FALSE,
cluster_rows = hc_mean_cells,
row_dend_reorder = FALSE,
column_dend_reorder = FALSE,
row_split = kk_cells,
show_heatmap_legend = FALSE,
show_column_names = FALSE,
column_title = "Gene pair clusters",
row_title = "Cells",
row_title_gp = gpar(fontsize = 20),
column_title_gp = gpar(fontsize = 20),
border = "black"
)
hh
grobh = grid.grabExpr(draw(hh))
pdf("output/split_heatmap_combined.pdf",height = 7, width = 11, useDingbats = FALSE)
cowplot::plot_grid(grob,
g_cells + theme(plot.margin = margin(2,0.5,0.2,-0.5,unit = "cm")) +
theme(strip.text = element_blank()),
g_mean + theme(plot.margin = margin(0,0,0,1.5, unit = "cm")) +
theme(strip.text = element_blank()) +
NULL
,
ncol = 2,
rel_heights = c(7,1),
rel_widths = c(9,1))
dev.off()## quartz_off_screen
## 2pdf("output/split_heatmap_combined_summarised.pdf",height = 8, width = 9, useDingbats = FALSE)
cowplot::plot_grid(grobh,
g_cells +
theme(plot.margin = margin(1.3,0.5,-0.2,-0.5,unit = "cm")) +
theme(strip.text = element_blank()),
g_mean +
theme(plot.margin = margin(0,0,0,1.5, unit = "cm")) +
theme(strip.text = element_blank()),
ncol = 2,
rel_heights = c(8,1),
rel_widths = c(8,1))
dev.off()## quartz_off_screen
## 2Gene ontology enrichment testing
if (!file.exists("output/GO_list.Rds")) {
library(GO.db)
library(org.Mm.eg.db)
keys = keys(org.Mm.eg.db)
columns(org.Mm.eg.db)
GO_info = select(org.Mm.eg.db, keys=keys, columns = c("SYMBOL", "GO"))
keep = GO_info$SYMBOL %in% rownames(counts)
table(keep)
GO_info_filt = GO_info[keep,]
# at least 10 genes in the term and less than 500
allTerms = names(which(table(GO_info_filt$GO) >= 10 & table(GO_info_filt$GO) <= 500))
GO_info_terms = select(GO.db, columns = columns(GO.db), keys = allTerms)
rownames(GO_info_terms) <- GO_info_terms$GOID
allTermNames = GO_info_terms[allTerms, "TERM"]
names(allTermNames) <- allTerms
GO_list = sapply(allTerms, function(term) {
print(term)
genes = GO_info_filt[GO_info_filt$GO == term, "SYMBOL"]
return(sort(unique(genes[!is.na(genes)])))
}, simplify = FALSE)
names(GO_list) <- allTermNames
saveRDS(GO_list, file = "output/GO_list.Rds")
} else {
GO_list = readRDS("output/GO_list.Rds")
}## [1] "GO:0000002"
## [1] "GO:0000012"
## [1] "GO:0000014"
## [1] "GO:0000027"
## [1] "GO:0000028"
## [1] "GO:0000030"
## [1] "GO:0000038"
## [1] "GO:0000045"
## [1] "GO:0000049"
## [1] "GO:0000055"
## [1] "GO:0000062"
## [1] "GO:0000070"
## [1] "GO:0000077"
## [1] "GO:0000079"
## [1] "GO:0000082"
## [1] "GO:0000086"
## [1] "GO:0000118"
## [1] "GO:0000123"
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## [1] "GO:0000781"
## [1] "GO:0000783"
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## [1] "GO:0000790"
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## [1] "GO:0000796"
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## [1] "GO:0003824"
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## [1] "GO:0005089"
## [1] "GO:0005092"
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## [1] "GO:2001256"
## [1] "GO:2001259"if (!file.exists("output/superclusterstotest_GO.Rds")) {
superclusterstotest_GO = lapply(geneClustMembers, function(set) {
print("testing..")
genesetGOtest(set, rownames(counts), GO_list)
}
)
saveRDS(superclusterstotest_GO, file = "output/superclusterstotest_GO.Rds")
} else {
superclusterstotest_GO <- readRDS("output/superclusterstotest_GO.Rds")
}## [1] "testing.."
## [1] "testing.."
## [1] "testing.."
## [1] "testing.."
## [1] "testing.."
## [1] "testing.."
## [1] "testing.."
## [1] "testing.."gList = lapply(superclusterstotest_GO, function(pval) {
df = data.frame(term = factor(names(pval), levels = c(names(pval), "")),
pval = pval)
df$label = df$term
df$label[pval != 1] <- ""
df_sorted = sort_df(df, "pval")[1:10,]
df_sorted$term = factor(df_sorted$term, levels = rev(df_sorted$term))
g = ggplot(df_sorted, aes(x = term, y = -log10(pval), fill = pval < 0.01)) +
theme_classic() +
geom_col() +
coord_flip() +
xlab("") +
ylab("-log10(P-value)") +
geom_hline(yintercept = -log10(0.01), colour = "red", linetype = "dashed", size = 1) +
scale_x_discrete(labels = function(x) str_wrap(x, width = 30)) +
scale_fill_manual(values = c("TRUE" = "darkgrey", "FALSE" = "black")) +
theme(legend.position = "none") +
NULL
return(g)
})
gTogether = sapply(seq_len(length(gList)), function(i){
g_1 = gList[[i]] +
theme(axis.text = element_text(size = 12))
n = ggtitle(paste0("Cluster ",i))
g_2 = gList_cells[[i]] + theme(title = element_text(size = 20)) +
coord_fixed()
pdf(paste0("output/go_cluster_plot_cluster_",i,".pdf"),
height = 7, width = 4.5)
scater::multiplot(g_2 + n, g_1 + ylab(""), layout = matrix(c(1,1,2,2,2), ncol = 1))
dev.off()
return(g_1 + g_2)
}, simplify = FALSE)sessionInfo()## R version 3.6.1 (2019-07-05)
## Platform: x86_64-apple-darwin18.6.0 (64-bit)
## Running under: macOS Mojave 10.14.6
##
## Matrix products: default
## BLAS/LAPACK: /usr/local/Cellar/openblas/0.3.6_1/lib/libopenblasp-r0.3.6.dylib
##
## locale:
## [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
##
## attached base packages:
## [1] grid parallel stats4 stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] cowplot_1.0.0 ggpubr_0.2.2
## [3] magrittr_1.5 patchwork_0.0.1
## [5] ggforce_0.3.0.9000 stringr_1.4.0
## [7] org.Mm.eg.db_3.8.2 GO.db_3.8.2
## [9] AnnotationDbi_1.46.0 ComplexHeatmap_2.0.0
## [11] dynamicTreeCut_1.63-1 scattermore_0.4
## [13] reshape_0.8.8 scran_1.12.1
## [15] scater_1.12.2 SingleCellExperiment_1.6.0
## [17] SummarizedExperiment_1.14.1 DelayedArray_0.10.0
## [19] BiocParallel_1.18.0 matrixStats_0.54.0
## [21] Biobase_2.44.0 GenomicRanges_1.36.0
## [23] GenomeInfoDb_1.20.0 IRanges_2.18.1
## [25] S4Vectors_0.22.0 BiocGenerics_0.30.0
## [27] gplots_3.0.1.1 ggplot2_3.2.0
## [29] DCARS_0.3.5
##
## loaded via a namespace (and not attached):
## [1] ggbeeswarm_0.6.0 colorspace_1.4-1
## [3] deldir_0.1-23 ggsignif_0.6.0
## [5] rjson_0.2.20 circlize_0.4.6
## [7] XVector_0.24.0 GlobalOptions_0.1.0
## [9] BiocNeighbors_1.2.0 clue_0.3-57
## [11] farver_1.1.0 bit64_0.9-7
## [13] codetools_0.2-16 knitr_1.23
## [15] polyclip_1.10-0 zeallot_0.1.0
## [17] cluster_2.1.0 png_0.1-7
## [19] compiler_3.6.1 dqrng_0.2.1
## [21] backports_1.1.4 assertthat_0.2.1
## [23] Matrix_1.2-17 lazyeval_0.2.2
## [25] limma_3.40.6 tweenr_1.0.1
## [27] BiocSingular_1.0.0 htmltools_0.3.6
## [29] tools_3.6.1 rsvd_1.0.2
## [31] igraph_1.2.4.1 gtable_0.3.0
## [33] glue_1.3.1 GenomeInfoDbData_1.2.1
## [35] reshape2_1.4.3 dplyr_0.8.3
## [37] Rcpp_1.0.2 vctrs_0.2.0
## [39] gdata_2.18.0 DelayedMatrixStats_1.6.0
## [41] xfun_0.8 irlba_2.3.3
## [43] gtools_3.8.1 statmod_1.4.32
## [45] edgeR_3.26.6 zlibbioc_1.30.0
## [47] MASS_7.3-51.4 scales_1.0.0
## [49] RColorBrewer_1.1-2 yaml_2.2.0
## [51] memoise_1.1.0 gridExtra_2.3
## [53] stringi_1.4.3 RSQLite_2.1.2
## [55] caTools_1.17.1.2 shape_1.4.4
## [57] rlang_0.4.0 pkgconfig_2.0.2
## [59] bitops_1.0-6 evaluate_0.14
## [61] lattice_0.20-38 purrr_0.3.2
## [63] labeling_0.3 bit_1.1-14
## [65] tidyselect_0.2.5 plyr_1.8.4
## [67] R6_2.4.0 DBI_1.0.0
## [69] pillar_1.4.2 withr_2.1.2
## [71] RCurl_1.95-4.12 tibble_2.1.3
## [73] crayon_1.3.4 KernSmooth_2.23-15
## [75] rmarkdown_1.14 viridis_0.5.1
## [77] GetoptLong_0.1.7 locfit_1.5-9.1
## [79] blob_1.2.0 digest_0.6.20
## [81] munsell_0.5.0 beeswarm_0.2.3
## [83] viridisLite_0.3.0 vipor_0.4.5